[ { "biomarker_id": "AN6278-1", "biomarker_component": [ { "biomarker": "increased IL6 level", "assessed_biomarker_entity": { "recommended_name": "Interleukin-6", "synonyms": [ { "synonym": "IL-6" }, { "synonym": "B-cell stimulatory factor 2" }, { "synonym": "BSF-2" }, { "synonym": "CTL differentiation factor" }, { "synonym": "CDF" }, { "synonym": "Hybridoma growth factor" }, { "synonym": "Interferon beta-2" }, { "synonym": "IFN-beta-2" } ] }, "assessed_biomarker_entity_id": "UPKB:P05231", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "26881-3" } ], "evidence_source": [ { "id": "10914713", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/10914713", "evidence_list": [ { "evidence": "Univariate analysis of all patients demonstrated that an extent of disease (EOD) on bone scanning > or = 1, IL-6 > or = 7 pg/ml, PS > or = 1, PSA > 100 ng/ml, and ALP > 620 IU/liter were associated with a significantly lower survival rate than their respective counterparts. In multivariate analysis, however, the only two significant prognostic factors were EOD and IL-6. These results indicate that the serum IL-6 level is a significant prognostic factor for prostate cancer as well as EOD." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, "synonyms": [ { "id": "DOID:10283", "name": "prostate neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "NGP - new growth of prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "tumor of the prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostate cancer, familial", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostatic neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "malignant tumor of the prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "hereditary prostate cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostatic cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" } ] }, "evidence_source": [ { "id": "10914713", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/10914713", "evidence_list": [ { "evidence": "Univariate analysis of all patients demonstrated that an extent of disease (EOD) on bone scanning > or = 1, IL-6 > or = 7 pg/ml, PS > or = 1, PSA > 100 ng/ml, and ALP > 620 IU/liter were associated with a significantly lower survival rate than their respective counterparts. In multivariate analysis, however, the only two significant prognostic factors were EOD and IL-6. These results indicate that the serum IL-6 level is a significant prognostic factor for prostate cancer as well as EOD." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Serum interleukin 6 as a prognostic factor in patients with prostate cancer.", "journal": "Clinical cancer research : an official journal of the American Association for Cancer Research", "authors": "Nakashima J, Tachibana M, Horiguchi Y, Oya M, Ohigashi T, Asakura H, Murai M", "date": "2000-07-29", "evidence": [], "reference": [ { "id": "10914713", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/10914713" } ] } ], "biomarker_canonical_id": "AN6278", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6278-5", "biomarker_component": [ { "biomarker": "increased IL6 level", "assessed_biomarker_entity": { "recommended_name": "Interleukin-6", "synonyms": [ { "synonym": "IL-6" }, { "synonym": "B-cell stimulatory factor 2" }, { "synonym": "BSF-2" }, { "synonym": "CTL differentiation factor" }, { "synonym": "CDF" }, { "synonym": "Hybridoma growth factor" }, { "synonym": "Interferon beta-2" }, { "synonym": "IFN-beta-2" } ] }, "assessed_biomarker_entity_id": "UPKB:P05231", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "26881-3" } ], "evidence_source": [ { "id": "32479790", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32479790", "evidence_list": [ { "evidence": "IL-6 plays multifaceted roles in regulation of vascular leakage, complement activation, and coagulation pathways, which ultimately causes poor outcomes for acute respiratory distress syndrome, multiple organ dysfunction syndrome, and SARS." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32369209", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32369209", "evidence_list": [ { "evidence": "Low lymphocytes, increased IL-6, CRP, PCT, D dimer, and LDH, these finds were similar to previous studies. The increase of these inflammatory indexes indicates that the infected patients were in inflammatory state, which may be closely related to the inflammatory storm. The increase of the cancer biomarkers in patients with COVID-19, especially in severe and critical patients, suggests that inflammation is closely related to the development of COVID-19." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32259560", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32259560", "evidence_list": [ { "evidence": "Serial measurement of circulating IL-6 levels may be important in identifying disease progression among COVID-19-infected patients." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32428990", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32428990", "evidence_list": [ { "evidence": "The decrease of IL-6 was closely related to treatment effectiveness, while the increase of IL-6 indicated disease exacerbation. Collectively, the dynamic change of IL-6 level can be used as a marker for disease monitoring in patients with severe COVID-19." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32677844", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32677844", "evidence_list": [ { "evidence": "Elevated levels of IL-6, D-dimer, CRP, LDH, and ferritin all had an independent increased risk for the clinical outcomes assessed (ICU admission, invasive ventilatory support and death), which were statistically significant." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32438331", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32438331", "evidence_list": [ { "evidence": "Clinical biomarkers for chronic inflammation, in particular Interleukin-6, predict the severity of COVID-19." }, { "evidence": "A deep network analysis has suggested clinical biomarkers predicting the higher risk of severe COVID-19 infection: Hypertension, elevated serum Alanine aminotransferase, high Interleukin-6, and low Lymphocytes count. In particular, patients with diabetes, but also those with prediabetic state, deserve special attention." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32475810", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32475810", "evidence_list": [ { "evidence": "C-reactive protein, serum amyloid A, interleukin-6, lactate dehydrogenase, neutrophil-to-lymphocyte ratio, D-dimer, cardiac troponin, and renal biomarkers showed significantly higher levels in patients with severe complications of COVID-19 infection compared to their non-severe counterparts." }, { "evidence": "Since the proportionate rise of IL-6 is correlated with disease severity, this study can prove ground-breaking." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32234467", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32234467", "evidence_list": [ { "evidence": "Interleukin-6 (IL-6) plays an important role in cytokine release syndrome. If it is possible to block the signal transduction pathway of IL-6, it is expected to become a new method for the treatment of severe COVID-19 patients." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32442528", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32442528", "evidence_list": [ { "evidence": "findings in this study include determining independent associations between biomarkers for inflammation (interleukin-6) and thrombosis (D-dimer) and mortality." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32161940", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32161940", "evidence_list": [ { "evidence": "lower lymphocyte counts, higher leukocyte counts and neutrophil-lymphocyte ratio (NLR), lower monocytes, eosinophils, and basophils elevated inflammatory cytokines. T cells significantly decreased, helper T (Th) cells and suppressor T cells were below normal levels naive Th cells increased and memory Th cells decreased. lower levels of regulatory T cells." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32425269", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32425269", "evidence_list": [ { "evidence": "The maximal level of IL-6, followed by CRP level, was highly predictive of the need for mechanical ventilation. This suggests the possibility of using IL-6 or CRP level to guide escalation of treatment in patients with COVID-19-related hyperinflammatory syndrome." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32385523", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32385523", "evidence_list": [ { "evidence": "Up-regulated IL-6 levels may serve as a potential marker for predicting progression of COVID19 patients." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32181911", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32181911", "evidence_list": [ { "evidence": "IL-6 and d-D were closely related to the occurrence of severe COVID-19 in the adult patients, and their combined detection had the highest specificity and sensitivity for early prediction of the severity of COVID-19 patients, which has important clinical value." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32344321", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32344321", "evidence_list": [ { "evidence": "The serum levels of IL-6 and CRP can effectively assess disease severity and predict outcome in patients with COVID-19." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32286245", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32286245", "evidence_list": [ { "evidence": "In hospitalized patients with respiratory distress, we recommend clinicians closely monitor WBC count, lymphocyte count, platelet count, IL-6 and serum ferritin as markers for potential progression to critical illness." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32430456", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32430456", "evidence_list": [ { "evidence": "The mean of glycemia during hospitalization was 10.65 0.84 mmol/L in the no insulin infusion group and 7.69 1.85 mmol/L in the insulin infusion group. At baseline, IL-6 and D-dimer levels were significantly higher in the hyperglycemic group than in the normoglycemic group (P < 0.001). Even though all patients were on standard treatment for COVID-19 infection, IL-6 and D-dimer levels persisted higher in patients with hyperglycemia during hospitalization." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32511562", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32511562", "evidence_list": [ { "evidence": "COVID-19 is associated with high levels of IL-6, TNF-a, IL-1b, and CXCL8/IL-8. IL-6 was one of the most robust prognostic markers of survival. It remained independently associated with severity and predictive of outcome. Furthermore, elevated TNF-a, known to contribute to organ damage, was also a strong predictor of poor outcome." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:0080600", "recommended_name": { "id": "DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, "synonyms": [ { "id": "DOID:0080600", "name": "SARS-CoV-2 infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan coronavirus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "COVID19", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan seafood market pneumonia virus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019-nCoV infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019 Novel Coronavirus (2019-nCoV)", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" } ] }, "evidence_source": [ { "id": "32479790", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32479790", "evidence_list": [ { "evidence": "IL-6 plays multifaceted roles in regulation of vascular leakage, complement activation, and coagulation pathways, which ultimately causes poor outcomes for acute respiratory distress syndrome, multiple organ dysfunction syndrome, and SARS." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32369209", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32369209", "evidence_list": [ { "evidence": "Low lymphocytes, increased IL-6, CRP, PCT, D dimer, and LDH, these finds were similar to previous studies. The increase of these inflammatory indexes indicates that the infected patients were in inflammatory state, which may be closely related to the inflammatory storm. The increase of the cancer biomarkers in patients with COVID-19, especially in severe and critical patients, suggests that inflammation is closely related to the development of COVID-19." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32259560", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32259560", "evidence_list": [ { "evidence": "Serial measurement of circulating IL-6 levels may be important in identifying disease progression among COVID-19-infected patients." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32428990", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32428990", "evidence_list": [ { "evidence": "The decrease of IL-6 was closely related to treatment effectiveness, while the increase of IL-6 indicated disease exacerbation. Collectively, the dynamic change of IL-6 level can be used as a marker for disease monitoring in patients with severe COVID-19." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32677844", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32677844", "evidence_list": [ { "evidence": "Elevated levels of IL-6, D-dimer, CRP, LDH, and ferritin all had an independent increased risk for the clinical outcomes assessed (ICU admission, invasive ventilatory support and death), which were statistically significant." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32438331", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32438331", "evidence_list": [ { "evidence": "Clinical biomarkers for chronic inflammation, in particular Interleukin-6, predict the severity of COVID-19." }, { "evidence": "A deep network analysis has suggested clinical biomarkers predicting the higher risk of severe COVID-19 infection: Hypertension, elevated serum Alanine aminotransferase, high Interleukin-6, and low Lymphocytes count. In particular, patients with diabetes, but also those with prediabetic state, deserve special attention." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32475810", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32475810", "evidence_list": [ { "evidence": "C-reactive protein, serum amyloid A, interleukin-6, lactate dehydrogenase, neutrophil-to-lymphocyte ratio, D-dimer, cardiac troponin, and renal biomarkers showed significantly higher levels in patients with severe complications of COVID-19 infection compared to their non-severe counterparts." }, { "evidence": "Since the proportionate rise of IL-6 is correlated with disease severity, this study can prove ground-breaking." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32234467", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32234467", "evidence_list": [ { "evidence": "Interleukin-6 (IL-6) plays an important role in cytokine release syndrome. If it is possible to block the signal transduction pathway of IL-6, it is expected to become a new method for the treatment of severe COVID-19 patients." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32442528", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32442528", "evidence_list": [ { "evidence": "findings in this study include determining independent associations between biomarkers for inflammation (interleukin-6) and thrombosis (D-dimer) and mortality." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32161940", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32161940", "evidence_list": [ { "evidence": "lower lymphocyte counts, higher leukocyte counts and neutrophil-lymphocyte ratio (NLR), lower monocytes, eosinophils, and basophils elevated inflammatory cytokines. T cells significantly decreased, helper T (Th) cells and suppressor T cells were below normal levels naive Th cells increased and memory Th cells decreased. lower levels of regulatory T cells." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32425269", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32425269", "evidence_list": [ { "evidence": "The maximal level of IL-6, followed by CRP level, was highly predictive of the need for mechanical ventilation. This suggests the possibility of using IL-6 or CRP level to guide escalation of treatment in patients with COVID-19-related hyperinflammatory syndrome." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32385523", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32385523", "evidence_list": [ { "evidence": "Up-regulated IL-6 levels may serve as a potential marker for predicting progression of COVID19 patients." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32181911", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32181911", "evidence_list": [ { "evidence": "IL-6 and d-D were closely related to the occurrence of severe COVID-19 in the adult patients, and their combined detection had the highest specificity and sensitivity for early prediction of the severity of COVID-19 patients, which has important clinical value." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32344321", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32344321", "evidence_list": [ { "evidence": "The serum levels of IL-6 and CRP can effectively assess disease severity and predict outcome in patients with COVID-19." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32286245", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32286245", "evidence_list": [ { "evidence": "In hospitalized patients with respiratory distress, we recommend clinicians closely monitor WBC count, lymphocyte count, platelet count, IL-6 and serum ferritin as markers for potential progression to critical illness." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32430456", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32430456", "evidence_list": [ { "evidence": "The mean of glycemia during hospitalization was 10.65 0.84 mmol/L in the no insulin infusion group and 7.69 1.85 mmol/L in the insulin infusion group. At baseline, IL-6 and D-dimer levels were significantly higher in the hyperglycemic group than in the normoglycemic group (P < 0.001). Even though all patients were on standard treatment for COVID-19 infection, IL-6 and D-dimer levels persisted higher in patients with hyperglycemia during hospitalization." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32511562", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32511562", "evidence_list": [ { "evidence": "COVID-19 is associated with high levels of IL-6, TNF-a, IL-1b, and CXCL8/IL-8. IL-6 was one of the most robust prognostic markers of survival. It remained independently associated with severity and predictive of outcome. Furthermore, elevated TNF-a, known to contribute to organ damage, was also a strong predictor of poor outcome." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "33303843", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/33303843", "evidence_list": [ { "evidence": "Elevated levels of pro-inflammatory cytokines were present in patients with severe COVID19. IL-6 and MCP-1 were inversely correlated with P/F with the largest AUC in ROC analyses and should be further explored as biomarkers to identify patients at risk for severe RF and as targets for improved treatment strategies." } ], "tags": [ { "tag": "condition" }, { "tag": "best_biomarker_role" } ] }, { "id": "32505227", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32505227", "evidence_list": [ { "evidence": "Other consistently reported markers in non-survivors are increased procalcitonin (PCT) and IL-6 levels, as well as increased serum urea, creatinine, cystatin C, direct bilirubin, and cholinesterase." } ], "tags": [ { "tag": "condition" }, { "tag": "best_biomarker_role" } ] }, { "id": "33349241", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/33349241", "evidence_list": [ { "evidence": "Significant correlations were found about age, IL2R, IL-6, IL-8, IL-10, TNFα, CRP, ferroprotein, PCT, LC, NC, and EC. PCT (R = -0.650), CRP (R = -0.604), NC (R = -0.585), age (R = -0.564), LC (R = 0.56), IL-6 (R = -0.535), IL2R (R = -0.534) and ferroprotein (R = -0.508) were highly correlated." } ], "tags": [ { "tag": "condition" }, { "tag": "best_biomarker_role" } ] }, { "id": "32503382", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32503382", "evidence_list": [ { "evidence": "Erythrocyte sedimentation rate (ESR) (R=0.55, p < .01) was positively associated with CT severity scores. To sum up, we can conclude from the analysis of published studies that hematological (lymphocyte count, neutrophil count, and NLR), inflammatory (CRP, ESR, IL-6), and especially biochemical (D-dimer, Troponins, CK) parameters correlate with severe prognosis or exitus in COVID-19 patients and can therefore be used as predictive biomarkers." } ], "tags": [ { "tag": "condition" }, { "tag": "best_biomarker_role" } ] }, { "id": "32576222", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32576222", "evidence_list": [ { "evidence": "Levels of VEGF-D, TNF-alpha, SCF, LIF, IL-2, IL-4, IL-6, IL-8, IL-10, IL-15, IL-17A, IL-18, IL-1 beta, and IFN-gamma were significantly higher in the critical group than in the severe group (Table 1)." } ], "tags": [ { "tag": "condition" }, { "tag": "best_biomarker_role" } ] }, { "id": "32503877", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32503877", "evidence_list": [ { "evidence": "Analysis revealed significantly elevated BTK activity, as evidenced by autophosphorylation, and increased IL-6 production." } ], "tags": [ { "tag": "condition" }, { "tag": "best_biomarker_role" } ] } ], "citation": [ { "title": "Clinical characteristics and risk factors associated with COVID-19 disease severity in patients with cancer in Wuhan, China: a multicentre, retrospective, cohort study.", "journal": "The Lancet. Oncology", "authors": "Tian J, Yuan X, Xiao J, Zhong Q, Yang C, Liu B, Cai Y, Lu Z, Wang J, Wang Y, Liu S, Cheng B, Wang J, Zhang M, Wang L, Niu S, Yao Z, Deng X, Zhou F, Wei W, Li Q, Chen X, Chen W, Yang Q, Wu S, Fan J, Shu B, Hu Z, Wang S, Yang XP, Liu W, Miao X, Wang Z", "date": "2020-06-02", "evidence": [], "reference": [ { "id": "32479790", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32479790" } ] }, { "title": "Clinical characteristics and outcomes of cancer patients with COVID-19.", "journal": "Journal of medical virology", "authors": "Yang F, Shi S, Zhu J, Shi J, Dai K, Chen X", "date": "2020-05-06", "evidence": [], "reference": [ { "id": "32369209", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32369209" } ] }, { "title": "Interleukin-6 as a potential biomarker of COVID-19 progression.", "journal": "Medecine et maladies infectieuses", "authors": "Ulhaq ZS, Soraya GV", "date": "2020-04-08", "evidence": [], "reference": [ { "id": "32259560", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32259560" } ] }, { "title": "The role of interleukin-6 in monitoring severe case of coronavirus disease 2019.", "journal": "EMBO molecular medicine", "authors": "Liu T, Zhang J, Yang Y, Ma H, Li Z, Zhang J, Cheng J, Zhang X, Zhao Y, Xia Z, Zhang L, Wu G, Yi J", "date": "2020-05-20", "evidence": [], "reference": [ { "id": "32428990", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32428990" } ] }, { "title": "The association between biomarkers and clinical outcomes in novel coronavirus pneumonia in a US cohort.", "journal": "Biomarkers in medicine", "authors": "Ayanian S, Reyes J, Lynn L, Teufel K", "date": "2020-07-18", "evidence": [], "reference": [ { "id": "32677844", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32677844" } ] }, { "title": "Diabetes and metabolic syndrome as risk factors for COVID-19.", "journal": "Diabetes & metabolic syndrome", "authors": "Marhl M, Grubelnik V, Magdič M, Markovič R", "date": "2020-05-22", "evidence": [], "reference": [ { "id": "32438331", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32438331" } ] }, { "title": "The role of biomarkers in diagnosis of COVID-19 - A systematic review.", "journal": "Life sciences", "authors": "Kermali M, Khalsa RK, Pillai K, Ismail Z, Harky A", "date": "2020-06-02", "evidence": [], "reference": [ { "id": "32475810", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32475810" } ] }, { "title": "Cytokine release syndrome in severe COVID-19: interleukin-6 receptor antagonist tocilizumab may be the key to reduce mortality.", "journal": "International journal of antimicrobial agents", "authors": "Zhang C, Wu Z, Li JW, Zhao H, Wang GQ", "date": "2020-04-03", "evidence": [], "reference": [ { "id": "32234467", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32234467" } ] }, { "title": "Epidemiology, clinical course, and outcomes of critically ill adults with COVID-19 in New York City: a prospective cohort study.", "journal": "Lancet (London, England)", "authors": "Cummings MJ, Baldwin MR, Abrams D, Jacobson SD, Meyer BJ, Balough EM, Aaron JG, Claassen J, Rabbani LE, Hastie J, Hochman BR, Salazar-Schicchi J, Yip NH, Brodie D, O'Donnell MR", "date": "2020-05-23", "evidence": [], "reference": [ { "id": "32442528", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32442528" } ] }, { "title": "Dysregulation of Immune Response in Patients With Coronavirus 2019 (COVID-19) in Wuhan, China.", "journal": "Clinical infectious diseases : an official publication of the Infectious Diseases Society of America", "authors": "Qin C, Zhou L, Hu Z, Zhang S, Yang S, Tao Y, Xie C, Ma K, Shang K, Wang W, Tian DS", "date": "2020-03-13", "evidence": [], "reference": [ { "id": "32161940", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32161940" } ] }, { "title": "Elevated levels of IL-6 and CRP predict the need for mechanical ventilation in COVID-19.", "journal": "The Journal of allergy and clinical immunology", "authors": "Herold T, Jurinovic V, Arnreich C, Lipworth BJ, Hellmuth JC, von Bergwelt-Baildon M, Klein M, Weinberger T", "date": "2020-05-20", "evidence": [], "reference": [ { "id": "32425269", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32425269" } ] }, { "title": "IL-6 may be a good biomarker for earlier detection of COVID-19 progression.", "journal": "Intensive care medicine", "authors": "Wang C, Fei D, Li X, Zhao M, Yu K", "date": "2020-05-10", "evidence": [], "reference": [ { "id": "32385523", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32385523" } ] }, { "title": "Diagnostic utility of clinical laboratory data determinations for patients with the severe COVID-19.", "journal": "Journal of medical virology", "authors": "Gao Y, Li T, Han M, Li X, Wu D, Xu Y, Zhu Y, Liu Y, Wang X, Wang L", "date": "2020-03-18", "evidence": [], "reference": [ { "id": "32181911", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32181911" } ] }, { "title": "Prognostic value of interleukin-6, C-reactive protein, and procalcitonin in patients with COVID-19.", "journal": "Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology", "authors": "Liu F, Li L, Xu M, Wu J, Luo D, Zhu Y, Li B, Song X, Zhou X", "date": "2020-04-29", "evidence": [], "reference": [ { "id": "32344321", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32344321" } ] }, { "title": "Hematologic, biochemical and immune biomarker abnormalities associated with severe illness and mortality in coronavirus disease 2019 (COVID-19): a meta-analysis.", "journal": "Clinical chemistry and laboratory medicine", "authors": "Henry BM, de Oliveira MHS, Benoit S, Plebani M, Lippi G", "date": "2020-04-15", "evidence": [], "reference": [ { "id": "32286245", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32286245" } ] }, { "title": "Outcomes in Patients With Hyperglycemia Affected by COVID-19: Can We Do More on Glycemic Control?", "journal": "Diabetes care", "authors": "Sardu C, D'Onofrio N, Balestrieri ML, Barbieri M, Rizzo MR, Messina V, Maggi P, Coppola N, Paolisso G, Marfella R", "date": "2020-05-21", "evidence": [], "reference": [ { "id": "32430456", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32430456" } ] }, { "title": "An inflammatory cytokine signature helps predict COVID-19 severity and death.", "journal": "medRxiv : the preprint server for health sciences", "authors": "Del Valle DM, Kim-Schulze S, Hsin-Hui H, Beckmann ND, Nirenberg S, Wang B, Lavin Y, Swartz T, Madduri D, Stock A, Marron T, Xie H, Patel MK, van Oekelen O, Rahman A, Kovatch P, Aberg J, Schadt E, Jagannath S, Mazumdar M, Charney A, Firpo-Betancourt A, Mendu DR, Jhang J, Reich D, Sigel K, Cordon-Cardo C, Feldmann M, Parekh S, Merad M, Gnjatic S", "date": "2020-06-09", "evidence": [], "reference": [ { "id": "32511562", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32511562" } ] }, { "title": "Increased interleukin-6 and macrophage chemoattractant protein-1 are associated with respiratory failure in COVID-19.", "journal": "Scientific reports", "authors": "Jøntvedt Jørgensen M, Holter JC, Christensen EE, Schjalm C, Tonby K, Pischke SE, Jenum S, Skeie LG, Nur S, Lind A, Opsand H, Enersen TB, Grøndahl R, Hermann A, Dudman S, Muller F, Ueland T, Mollnes TE, Aukrust P, Heggelund L, Holten AR, Dyrhol-Riise AM", "date": "2020-12-12", "evidence": [], "reference": [ { "id": "33303843", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/33303843" } ] }, { "title": "Immunology of COVID-19: Current State of the Science.", "journal": "Immunity", "authors": "Vabret N, Britton GJ, Gruber C, Hegde S, Kim J, Kuksin M, Levantovsky R, Malle L, Moreira A, Park MD, Pia L, Risson E, Saffern M, Salomé B, Esai Selvan M, Spindler MP, Tan J, van der Heide V, Gregory JK, Alexandropoulos K, Bhardwaj N, Brown BD, Greenbaum B, Gümüş ZH, Homann D, Horowitz A, Kamphorst AO, Curotto de Lafaille MA, Mehandru S, Merad M, Samstein RM, None None", "date": "2020-06-09", "evidence": [], "reference": [ { "id": "32505227", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32505227" } ] }, { "title": "Correlation analysis between disease severity and inflammation-related parameters in patients with COVID-19: a retrospective study.", "journal": "BMC infectious diseases", "authors": "Gong J, Dong H, Xia QS, Huang ZY, Wang DK, Zhao Y, Liu WH, Tu SH, Zhang MM, Wang Q, Lu FE", "date": "2020-12-23", "evidence": [], "reference": [ { "id": "33349241", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/33349241" } ] }, { "title": "Biomarkers associated with COVID-19 disease progression.", "journal": "Critical reviews in clinical laboratory sciences", "authors": "Ponti G, Maccaferri M, Ruini C, Tomasi A, Ozben T", "date": "2020-06-07", "evidence": [], "reference": [ { "id": "32503382", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32503382" } ] }, { "title": "VEGF-D: a novel biomarker for detection of COVID-19 progression.", "journal": "Critical care (London, England)", "authors": "Kong Y, Han J, Wu X, Zeng H, Liu J, Zhang H", "date": "2020-06-25", "evidence": [], "reference": [ { "id": "32576222", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32576222" } ] }, { "title": "Inhibition of Bruton tyrosine kinase in patients with severe COVID-19.", "journal": "Science immunology", "authors": "Roschewski M, Lionakis MS, Sharman JP, Roswarski J, Goy A, Monticelli MA, Roshon M, Wrzesinski SH, Desai JV, Zarakas MA, Collen J, Rose K, Hamdy A, Izumi R, Wright GW, Chung KK, Baselga J, Staudt LM, Wilson WH", "date": "2020-06-07", "evidence": [], "reference": [ { "id": "32503877", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32503877" } ] } ], "biomarker_canonical_id": "AN6278", "score": 3.8, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 9 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "c": "condition", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6278-2", "biomarker_component": [ { "biomarker": "increased IL6 level", "assessed_biomarker_entity": { "recommended_name": "Interleukin-6", "synonyms": [ { "synonym": "IL-6" }, { "synonym": "B-cell stimulatory factor 2" }, { "synonym": "BSF-2" }, { "synonym": "CTL differentiation factor" }, { "synonym": "CDF" }, { "synonym": "Hybridoma growth factor" }, { "synonym": "Interferon beta-2" }, { "synonym": "IFN-beta-2" } ] }, "assessed_biomarker_entity_id": "UPKB:P05231", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "26881-3" } ], "evidence_source": [ { "id": "28848164", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/28848164", "evidence_list": [ { "evidence": "Our study is suggestive of S100A8/A9 and IL-6 being related to a persistent diabetes status post-surgically and of different pathophysiological mechanisms being involved in the post-surgical changes in the three groups, despite similar decreases in BMI." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:9351", "recommended_name": { "id": "DOID:9351", "name": "diabetes mellitus", "description": "A glucose metabolism disease that is characterized by chronic hyperglycaemia with disturbances of carbohydrate, fat and protein metabolism resulting from defects in insulin secretion, insulin action, or both.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_9351" }, "synonyms": [ { "id": "DOID:9351", "name": "diabetes", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_9351" } ] }, "evidence_source": [ { "id": "28848164", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/28848164", "evidence_list": [ { "evidence": "Our study is suggestive of S100A8/A9 and IL-6 being related to a persistent diabetes status post-surgically and of different pathophysiological mechanisms being involved in the post-surgical changes in the three groups, despite similar decreases in BMI." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "S100A8/A9 (Calprotectin), Interleukin-6, and C-Reactive Protein in Obesity and Diabetes before and after Roux-en-Y Gastric Bypass Surgery.", "journal": "Obesity facts", "authors": "Lylloff L, Bathum L, Madsbad S, Grundtvig JLG, Nordgaard-Lassen I, Fenger M", "date": "2017-08-30", "evidence": [], "reference": [ { "id": "28848164", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/28848164" } ] } ], "biomarker_canonical_id": "AN6278", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6278-3", "biomarker_component": [ { "biomarker": "increased IL6 level", "assessed_biomarker_entity": { "recommended_name": "Interleukin-6", "synonyms": [ { "synonym": "IL-6" }, { "synonym": "B-cell stimulatory factor 2" }, { "synonym": "BSF-2" }, { "synonym": "CTL differentiation factor" }, { "synonym": "CDF" }, { "synonym": "Hybridoma growth factor" }, { "synonym": "Interferon beta-2" }, { "synonym": "IFN-beta-2" } ] }, "assessed_biomarker_entity_id": "UPKB:P05231", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "26881-3" } ], "evidence_source": [ { "id": "31772933", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31772933", "evidence_list": [ { "evidence": "Significantly higher IL-15 and IL-6 concentrations, HOMAIR, and markedly lower eGDR in newly diagnosed AD patients and first-degree relatives with positive anti-islet antibodies might suggest the role of these pro-inflammatory cytokines and insulin resistance in the pathogenesis of autoimmune diabetes. IL-15 and IL-6 might be used as biomarkers of the risk of autoimmune diabetes development." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "risk" } ], "condition": { "id": "DOID:0080846", "recommended_name": { "id": "DOID:0080846", "name": "autoimunne diabetes", "description": "A type 1 diabetes mellitus that is characterized by a less intensive autoimmune process, highly variable β-cell destruction, different degrees of insulin resistance and heterogeneous titre and pattern of islet autoantibody, sharing features with both type 1 and type 2 diabetes mellitus.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080846" }, "synonyms": [ { "id": "DOID:0080846", "name": "LADA", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080846" }, { "id": "DOID:0080846", "name": "type 1.5 diabetes", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080846" } ] }, "evidence_source": [ { "id": "31772933", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31772933", "evidence_list": [ { "evidence": "Significantly higher IL-15 and IL-6 concentrations, HOMAIR, and markedly lower eGDR in newly diagnosed AD patients and first-degree relatives with positive anti-islet antibodies might suggest the role of these pro-inflammatory cytokines and insulin resistance in the pathogenesis of autoimmune diabetes. IL-15 and IL-6 might be used as biomarkers of the risk of autoimmune diabetes development." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Interleukin-6 and Interleukin-15 as Possible Biomarkers of the Risk of Autoimmune Diabetes Development.", "journal": "BioMed research international", "authors": "Siewko K, Maciulewski R, Zielinska-Maciulewska A, Poplawska-Kita A, Szumowski P, Wawrusiewicz-Kurylonek N, Lipinska D, Milewski R, Gorska M, Kretowski A, Szelachowska M", "date": "2019-11-28", "evidence": [], "reference": [ { "id": "31772933", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31772933" } ] } ], "biomarker_canonical_id": "AN6278", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "f": "frequency", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6280-1", "biomarker_component": [ { "biomarker": "increased WBC count", "assessed_biomarker_entity": { "recommended_name": "White blood cell", "synonyms": [ { "synonym": "immune cell" }, { "synonym": "leucocyte" }, { "synonym": "white blood cell" } ] }, "assessed_biomarker_entity_id": "CO:CL_0000738", "assessed_entity_type": "cell", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "26464-8" }, { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "32286245", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32286245", "evidence_list": [ { "evidence": "In hospitalized patients with respiratory distress, we recommend clinicians closely monitor WBC count, lymphocyte count, platelet count, IL-6 and serum ferritin as markers for potential progression to critical illness." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "33349241", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/33349241", "evidence_list": [ { "evidence": "With following parameters such as age >67.5 years, IL2R >793.5U/mL, CRP >30.7ng/mL, ferroprotein >2252ug/L, WBC>9.5x10^9/L or NC >7.305x10^9/L, the progress of COVID-19 to critical stage should be closely observed and possibly prevented." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32161940", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32161940", "evidence_list": [ { "evidence": "Lower lymphocyte counts, higher leukocyte counts and neutrophil-lymphocyte ratio (NLR), lower monocytes, eosinophils, and basophils elevated inflammatory cytokines T cells significantly decreased, helper T (Th) cells and suppressor T cells were below normal levels naive Th cells increased and memory Th cells decreased lower levels of regulatory T cells." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32281668", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32281668", "evidence_list": [ { "evidence": "Patients with flu had higher WBC, granulocyte and granulocyte/lymphocyte ratio, compared with COVID-19 patients." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32282949", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32282949", "evidence_list": [ { "evidence": "A retrospective study including 187 patients with COVID-19 from another hospital in Wuhan showed that patients with high troponin-T levels had leukocytosis (P < .001), increased neutrophils (P < .001) and decreased lymphocytes (P = .01)." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32224151", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32224151", "evidence_list": [ { "evidence": "The blood count results showed anaemia in 21 (75%) patients, leucopaenia in 9 (32.1%) patients, and lymphopaenia in 23 (82.1%) patients. Patients developed severe clinical events; 6 (21.4%) patients were admitted to ICU, 10 (35.7%) patients had life-threatening complications, and 8 (28.6%) of the patients died." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32357994", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32357994", "evidence_list": [ { "evidence": "Post-COVID-19 infection, lower hemoglobin levels, higher total white blood cell (WBC) counts, and higher absolute neutrophil counts were associated with increased mortality (Table 3). Analysis of other serologic biomarkers demonstrated that elevated D-dimer, lactate, and lactate dehydrogenase (LDH) in patients were significantly correlated with dying (Table 3)." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "monitoring" } ], "condition": { "id": "DOID:0080600", "recommended_name": { "id": "DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, "synonyms": [ { "id": "DOID:0080600", "name": "SARS-CoV-2 infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan coronavirus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "COVID19", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan seafood market pneumonia virus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019-nCoV infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019 Novel Coronavirus (2019-nCoV)", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" } ] }, "evidence_source": [ { "id": "32286245", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32286245", "evidence_list": [ { "evidence": "In hospitalized patients with respiratory distress, we recommend clinicians closely monitor WBC count, lymphocyte count, platelet count, IL-6 and serum ferritin as markers for potential progression to critical illness." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "33349241", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/33349241", "evidence_list": [ { "evidence": "With following parameters such as age >67.5 years, IL2R >793.5U/mL, CRP >30.7ng/mL, ferroprotein >2252ug/L, WBC>9.5x10^9/L or NC >7.305x10^9/L, the progress of COVID-19 to critical stage should be closely observed and possibly prevented." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32161940", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32161940", "evidence_list": [ { "evidence": "Lower lymphocyte counts, higher leukocyte counts and neutrophil-lymphocyte ratio (NLR), lower monocytes, eosinophils, and basophils elevated inflammatory cytokines T cells significantly decreased, helper T (Th) cells and suppressor T cells were below normal levels naive Th cells increased and memory Th cells decreased lower levels of regulatory T cells." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32281668", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32281668", "evidence_list": [ { "evidence": "Patients with flu had higher WBC, granulocyte and granulocyte/lymphocyte ratio, compared with COVID-19 patients." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32282949", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32282949", "evidence_list": [ { "evidence": "A retrospective study including 187 patients with COVID-19 from another hospital in Wuhan showed that patients with high troponin-T levels had leukocytosis (P < .001), increased neutrophils (P < .001) and decreased lymphocytes (P = .01)." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32224151", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32224151", "evidence_list": [ { "evidence": "The blood count results showed anaemia in 21 (75%) patients, leucopaenia in 9 (32.1%) patients, and lymphopaenia in 23 (82.1%) patients. Patients developed severe clinical events; 6 (21.4%) patients were admitted to ICU, 10 (35.7%) patients had life-threatening complications, and 8 (28.6%) of the patients died." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32357994", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32357994", "evidence_list": [ { "evidence": "Post-COVID-19 infection, lower hemoglobin levels, higher total white blood cell (WBC) counts, and higher absolute neutrophil counts were associated with increased mortality (Table 3). Analysis of other serologic biomarkers demonstrated that elevated D-dimer, lactate, and lactate dehydrogenase (LDH) in patients were significantly correlated with dying (Table 3)." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Hematologic, biochemical and immune biomarker abnormalities associated with severe illness and mortality in coronavirus disease 2019 (COVID-19): a meta-analysis.", "journal": "Clinical chemistry and laboratory medicine", "authors": "Henry BM, de Oliveira MHS, Benoit S, Plebani M, Lippi G", "date": "2020-04-15", "evidence": [], "reference": [ { "id": "32286245", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32286245" } ] }, { "title": "Correlation analysis between disease severity and inflammation-related parameters in patients with COVID-19: a retrospective study.", "journal": "BMC infectious diseases", "authors": "Gong J, Dong H, Xia QS, Huang ZY, Wang DK, Zhao Y, Liu WH, Tu SH, Zhang MM, Wang Q, Lu FE", "date": "2020-12-23", "evidence": [], "reference": [ { "id": "33349241", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/33349241" } ] }, { "title": "Dysregulation of Immune Response in Patients With Coronavirus 2019 (COVID-19) in Wuhan, China.", "journal": "Clinical infectious diseases : an official publication of the Infectious Diseases Society of America", "authors": "Qin C, Zhou L, Hu Z, Zhang S, Yang S, Tao Y, Xie C, Ma K, Shang K, Wang W, Tian DS", "date": "2020-03-13", "evidence": [], "reference": [ { "id": "32161940", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32161940" } ] }, { "title": "C-reactive protein correlates with computed tomographic findings and predicts severe COVID-19 early.", "journal": "Journal of medical virology", "authors": "Tan C, Huang Y, Shi F, Tan K, Ma Q, Chen Y, Jiang X, Li X", "date": "2020-04-14", "evidence": [], "reference": [ { "id": "32281668", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32281668" } ] }, { "title": "Hematological findings and complications of COVID-19.", "journal": "American journal of hematology", "authors": "Terpos E, Ntanasis-Stathopoulos I, Elalamy I, Kastritis E, Sergentanis TN, Politou M, Psaltopoulou T, Gerotziafas G, Dimopoulos MA", "date": "2020-04-14", "evidence": [], "reference": [ { "id": "32282949", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32282949" } ] }, { "title": "Clinical characteristics of COVID-19-infected cancer patients: a retrospective case study in three hospitals within Wuhan, China.", "journal": "Annals of oncology : official journal of the European Society for Medical Oncology", "authors": "Zhang L, Zhu F, Xie L, Wang C, Wang J, Chen R, Jia P, Guan HQ, Peng L, Chen Y, Peng P, Zhang P, Chu Q, Shen Q, Wang Y, Xu SY, Zhao JP, Zhou M", "date": "2020-04-01", "evidence": [], "reference": [ { "id": "32224151", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32224151" } ] }, { "title": "Case Fatality Rate of Cancer Patients with COVID-19 in a New York Hospital System.", "journal": "Cancer discovery", "authors": "Mehta V, Goel S, Kabarriti R, Cole D, Goldfinger M, Acuna-Villaorduna A, Pradhan K, Thota R, Reissman S, Sparano JA, Gartrell BA, Smith RV, Ohri N, Garg M, Racine AD, Kalnicki S, Perez-Soler R, Halmos B, Verma A", "date": "2020-05-03", "evidence": [], "reference": [ { "id": "32357994", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32357994" } ] } ], "biomarker_canonical_id": "AN6280", "score": 3.2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 6 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6280-2", "biomarker_component": [ { "biomarker": "increased WBC count", "assessed_biomarker_entity": { "recommended_name": "White blood cell", "synonyms": [ { "synonym": "immune cell" }, { "synonym": "leucocyte" }, { "synonym": "white blood cell" } ] }, "assessed_biomarker_entity_id": "CO:CL_0000738", "assessed_entity_type": "cell", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "30073209", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30073209", "evidence_list": [ { "evidence": "The strength of this study is the robust association between leukocytosis and poor prognosis in a homogenous cohort of HNSCC, treated with concurrent cisplatin." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:11934", "recommended_name": { "id": "DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11934" }, "synonyms": [ { "id": "DOID:11934", "name": "head and neck neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11934" }, { "id": "DOID:11934", "name": "head/neck neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11934" }, { "id": "DOID:11934", "name": "head and neck tumours", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11934" }, { "id": "DOID:11934", "name": "tumor of head and neck", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11934" } ] }, "evidence_source": [ { "id": "30073209", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30073209", "evidence_list": [ { "evidence": "The strength of this study is the robust association between leukocytosis and poor prognosis in a homogenous cohort of HNSCC, treated with concurrent cisplatin." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Leukocytosis, prognosis biomarker in locally advanced head and neck cancer patients after chemoradiotherapy.", "journal": "Clinical and translational radiation oncology", "authors": "Schernberg A, Blanchard P, Chargari C, Ou D, Levy A, Gorphe P, Breuskin I, Atallah S, Caula A, Escande A, Janot F, Nguyen F, Temam S, Deutsch E, Tao Y", "date": "2018-08-04", "evidence": [], "reference": [ { "id": "30073209", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30073209" } ] } ], "biomarker_canonical_id": "AN6280", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "c": "condition", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6281-1", "biomarker_component": [ { "biomarker": "decreased LYMP count", "assessed_biomarker_entity": { "recommended_name": "Lymphocyte", "synonyms": [] }, "assessed_biomarker_entity_id": "CO:CL_0000542", "assessed_entity_type": "cell", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "26474-7" }, { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "32369209", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32369209", "evidence_list": [ { "evidence": "Our results showed that the laboratory tests of cancer patients had the following characteristics: low lymphocytes, increased IL-6, CRP, PCT, D dimer, and LDH. The increase of these inflammatory indexes indicates that the infected patients were in inflammatory state, which may be closely related to the inflammatory storm." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32277967", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32277967", "evidence_list": [ { "evidence": "Patients with higher initial SAA are more likely to have poor CT imaging. Our study indicated that SAA/L. CRP, SAA, and l are valuable in predicting the severity and distinguishing critically ill patients from mild ones." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32475810", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32475810", "evidence_list": [ { "evidence": "Lymphocytes and platelet count showed significantly lower levels in severe patients compared to non-severe patients." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32048163", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32048163", "evidence_list": [ { "evidence": "the combinations of the hypoalbuminemia, lymphopenia, and high concentrations of CRP and LDH in 2019-nCoV infected patients upon hospital admission may predict more severe acute lung injury." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32438331", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32438331", "evidence_list": [ { "evidence": "Biomarkers that predict the mortality of individual patients more than 10 days in advance with more than 90% accuracy: lactic dehydrogenase (LDH), lymphocyte and high-sensitivity C-reactive protein (hs-CRP). [DOI:10.1038/s42256-020-0180-7] Clinical biomarkers predicting the higher risk: Hypertension, elevated serum Alanine aminotransferase, high Interleukin-6, decreased Lymphocytes count." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32471703", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32471703", "evidence_list": [ { "evidence": "We propose that a few parameters, such Lymphocytes count, L/N ratio, SaO2 and CRP serum level can be used to assess the severity of COVID-19 in emergency room." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32352397", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32352397", "evidence_list": [ { "evidence": "In this study, the most important finding was that the neutrophil count, lymphocyte count and platelet count were independent risk factors for predicting the development of severe illness in COVID-19 patients." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32377400", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32377400", "evidence_list": [ { "evidence": "Lymphopenia is an effective and reliable indicator of the severity and hospitalization in COVID-19 patients." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32286245", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32286245", "evidence_list": [ { "evidence": "In hospitalized patients with respiratory distress, we recommend clinicians closely monitor WBC count, lymphocyte count, platelet count, IL-6 and serum ferritin as markers for potential progression to critical illness." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32277967", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32277967", "evidence_list": [ { "evidence": "SAA and Lymphocytes are sensitive indicators in evaluating the severity and prognosis of COVID-19." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32161940", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32161940", "evidence_list": [ { "evidence": "Biomarkers that predict the mortality of individual patients more than 10 days in advance with more than 90% accuracy: lactic dehydrogenase (LDH), lymphocyte and high-sensitivity C-reactive protein (hs-CRP). [DOI:10.1038/s42256-020-0180-7] Lower lymphocyte counts, higher leukocyte counts and neutrophil-lymphocyte ratio (NLR), lower monocytes, eosinophils, and basophils elevated inflammatory cytokines T cells significantly decreased, helper T (Th) cells and suppressor T cells were below normal levels naive Th cells increased and memory Th cells decreased lower levels of regulatory T cells." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32220650", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32220650", "evidence_list": [ { "evidence": "Besides radiographic presentations, variables that were associated significantly with severity of COVID-19 were decreased lymphocytes, elevated body temperature, and high levels of procalcitonin, D-dimer, and creatine kinase MB." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32077115", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32077115", "evidence_list": [ { "evidence": "Detailed clinical investigation of 140 hospitalized COVID-19 cases suggests eosinopenia together with lymphopenia may be a potential indicator for diagnosis." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32376308", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32376308", "evidence_list": [ { "evidence": "Lymphopenia is a prominent part of severe COVID-19 and a lymphocyte count of less than 1.5 x 10^9/L may be useful in predicting the severity clinical outcomes." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] }, { "biomarker": "Decreased LYMP count", "assessed_biomarker_entity": { "recommended_name": "Lymphocyte", "synonyms": [] }, "assessed_biomarker_entity_id": "CO:CL_0000542", "assessed_entity_type": "cell", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "2157-6" } ], "evidence_source": [ { "id": "32589600", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32589600", "evidence_list": [ { "evidence": "Many biomarkers have been associated with poor outcomes and represent a candidate for risk stratification models for predicting severe COVID-19 in order to guide clinical care. Among all, lymphopenia, thrombocytopenia, leucocytosis, CRP, PCT, LDH, AST, ALT, D-dimer, cTn represent the most predictive parameters of severe COVID-19" } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] }, { "biomarker": "Increased LMYPH count", "assessed_biomarker_entity": { "recommended_name": "Lymphocyte", "synonyms": [] }, "assessed_biomarker_entity_id": "CO:CL_0000542", "assessed_entity_type": "cell", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "75708-8" } ], "evidence_source": [ { "id": "32388230", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32388230", "evidence_list": [ { "evidence": "Patient 1: Lymphocyte count increased from 30 × 10^9/l to a peak of 177 × 10^9/l.Patient 2: Lymphocyte count increased from 22 × 10^9/l to 32 × 10^9/l.Patient 3: Lymphocyte count increased from 235 × 10^9/l to 253 × 10^9/l and peaked at 346 × 10^9/l.Patient 4: Lymphocyte count increased from 2.8 × 10^9/l to 8 × 10^9/l." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:0080600", "recommended_name": { "id": "DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, "synonyms": [ { "id": "DOID:0080600", "name": "SARS-CoV-2 infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan coronavirus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "COVID19", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan seafood market pneumonia virus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019-nCoV infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019 Novel Coronavirus (2019-nCoV)", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" } ] }, "evidence_source": [ { "id": "32369209", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32369209", "evidence_list": [ { "evidence": "Our results showed that the laboratory tests of cancer patients had the following characteristics: low lymphocytes, increased IL-6, CRP, PCT, D dimer, and LDH. The increase of these inflammatory indexes indicates that the infected patients were in inflammatory state, which may be closely related to the inflammatory storm." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32475810", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32475810", "evidence_list": [ { "evidence": "Lymphocytes and platelet count showed significantly lower levels in severe patients compared to non-severe patients." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32048163", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32048163", "evidence_list": [ { "evidence": "the combinations of the hypoalbuminemia, lymphopenia, and high concentrations of CRP and LDH in 2019-nCoV infected patients upon hospital admission may predict more severe acute lung injury." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32438331", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32438331", "evidence_list": [ { "evidence": "Biomarkers that predict the mortality of individual patients more than 10 days in advance with more than 90% accuracy: lactic dehydrogenase (LDH), lymphocyte and high-sensitivity C-reactive protein (hs-CRP). [DOI:10.1038/s42256-020-0180-7] Clinical biomarkers predicting the higher risk: Hypertension, elevated serum Alanine aminotransferase, high Interleukin-6, decreased Lymphocytes count." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32471703", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32471703", "evidence_list": [ { "evidence": "We propose that a few parameters, such Lymphocytes count, L/N ratio, SaO2 and CRP serum level can be used to assess the severity of COVID-19 in emergency room." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32352397", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32352397", "evidence_list": [ { "evidence": "In this study, the most important finding was that the neutrophil count, lymphocyte count and platelet count were independent risk factors for predicting the development of severe illness in COVID-19 patients." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32377400", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32377400", "evidence_list": [ { "evidence": "Lymphopenia is an effective and reliable indicator of the severity and hospitalization in COVID-19 patients." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32286245", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32286245", "evidence_list": [ { "evidence": "In hospitalized patients with respiratory distress, we recommend clinicians closely monitor WBC count, lymphocyte count, platelet count, IL-6 and serum ferritin as markers for potential progression to critical illness." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32161940", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32161940", "evidence_list": [ { "evidence": "Biomarkers that predict the mortality of individual patients more than 10 days in advance with more than 90% accuracy: lactic dehydrogenase (LDH), lymphocyte and high-sensitivity C-reactive protein (hs-CRP). [DOI:10.1038/s42256-020-0180-7] Lower lymphocyte counts, higher leukocyte counts and neutrophil-lymphocyte ratio (NLR), lower monocytes, eosinophils, and basophils elevated inflammatory cytokines T cells significantly decreased, helper T (Th) cells and suppressor T cells were below normal levels naive Th cells increased and memory Th cells decreased lower levels of regulatory T cells." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32220650", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32220650", "evidence_list": [ { "evidence": "Besides radiographic presentations, variables that were associated significantly with severity of COVID-19 were decreased lymphocytes, elevated body temperature, and high levels of procalcitonin, D-dimer, and creatine kinase MB." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32077115", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32077115", "evidence_list": [ { "evidence": "Detailed clinical investigation of 140 hospitalized COVID-19 cases suggests eosinopenia together with lymphopenia may be a potential indicator for diagnosis." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32376308", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32376308", "evidence_list": [ { "evidence": "Lymphopenia is a prominent part of severe COVID-19 and a lymphocyte count of less than 1.5 x 10^9/L may be useful in predicting the severity clinical outcomes." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32277967", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32277967", "evidence_list": [ { "evidence": "Patients with higher initial SAA are more likely to have poor CT imaging. Our study indicated that SAA/L. CRP, SAA, and l are valuable in predicting the severity and distinguishing critically ill patients from mild ones." }, { "evidence": "SAA and Lymphocytes are sensitive indicators in evaluating the severity and prognosis of COVID-19." } ], "tags": [ { "tag": "condition" }, { "tag": "best_biomarker_role" } ] }, { "id": "32589600", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32589600", "evidence_list": [ { "evidence": "Many biomarkers have been associated with poor outcomes and represent a candidate for risk stratification models for predicting severe COVID-19 in order to guide clinical care. Among all, lymphopenia, thrombocytopenia, leucocytosis, CRP, PCT, LDH, AST, ALT, D-dimer, cTn represent the most predictive parameters of severe COVID-19" } ], "tags": [ { "tag": "condition" }, { "tag": "best_biomarker_role" } ] }, { "id": "32388230", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32388230", "evidence_list": [ { "evidence": "Patient 1: Lymphocyte count increased from 30 × 10^9/l to a peak of 177 × 10^9/l.Patient 2: Lymphocyte count increased from 22 × 10^9/l to 32 × 10^9/l.Patient 3: Lymphocyte count increased from 235 × 10^9/l to 253 × 10^9/l and peaked at 346 × 10^9/l.Patient 4: Lymphocyte count increased from 2.8 × 10^9/l to 8 × 10^9/l." } ], "tags": [ { "tag": "condition" }, { "tag": "best_biomarker_role" } ] } ], "citation": [ { "title": "Clinical characteristics and outcomes of cancer patients with COVID-19.", "journal": "Journal of medical virology", "authors": "Yang F, Shi S, Zhu J, Shi J, Dai K, Chen X", "date": "2020-05-06", "evidence": [], "reference": [ { "id": "32369209", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32369209" } ] }, { "title": "Serum Amyloid A is a biomarker of severe Coronavirus Disease and poor prognosis.", "journal": "The Journal of infection", "authors": "Li H, Xiang X, Ren H, Xu L, Zhao L, Chen X, Long H, Wang Q, Wu Q", "date": "2020-04-12", "evidence": [], "reference": [ { "id": "32277967", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32277967" } ] }, { "title": "The role of biomarkers in diagnosis of COVID-19 - A systematic review.", "journal": "Life sciences", "authors": "Kermali M, Khalsa RK, Pillai K, Ismail Z, Harky A", "date": "2020-06-02", "evidence": [], "reference": [ { "id": "32475810", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32475810" } ] }, { "title": "Clinical and biochemical indexes from 2019-nCoV infected patients linked to viral loads and lung injury.", "journal": "Science China. Life sciences", "authors": "Liu Y, Yang Y, Zhang C, Huang F, Wang F, Yuan J, Wang Z, Li J, Li J, Feng C, Zhang Z, Wang L, Peng L, Chen L, Qin Y, Zhao D, Tan S, Yin L, Xu J, Zhou C, Jiang C, Liu L", "date": "2020-02-13", "evidence": [], "reference": [ { "id": "32048163", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32048163" } ] }, { "title": "Diabetes and metabolic syndrome as risk factors for COVID-19.", "journal": "Diabetes & metabolic syndrome", "authors": "Marhl M, Grubelnik V, Magdič M, Markovič R", "date": "2020-05-22", "evidence": [], "reference": [ { "id": "32438331", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32438331" } ] }, { "title": "Laboratory Biomarkers Predicting COVID-19 Severity in the Emergency Room.", "journal": "Archives of medical research", "authors": "Assandri R, Buscarini E, Canetta C, Scartabellati A, Viganò G, Montanelli A", "date": "2020-05-31", "evidence": [], "reference": [ { "id": "32471703", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32471703" } ] }, { "title": "The hemocyte counts as a potential biomarker for predicting disease progression in COVID-19: a retrospective study.", "journal": "Clinical chemistry and laboratory medicine", "authors": "Zheng Y, Zhang Y, Chi H, Chen S, Peng M, Luo L, Chen L, Li J, Shen B, Wang D", "date": "2020-05-01", "evidence": [], "reference": [ { "id": "32352397", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32352397" } ] }, { "title": "Correction: Lymphopenia predicts disease severity of COVID-19: a descriptive and predictive study.", "journal": "Signal transduction and targeted therapy", "authors": "Tan L, Wang Q, Zhang D, Ding J, Huang Q, Tang YQ, Wang Q, Miao H", "date": "2020-05-08", "evidence": [], "reference": [ { "id": "32377400", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32377400" } ] }, { "title": "Hematologic, biochemical and immune biomarker abnormalities associated with severe illness and mortality in coronavirus disease 2019 (COVID-19): a meta-analysis.", "journal": "Clinical chemistry and laboratory medicine", "authors": "Henry BM, de Oliveira MHS, Benoit S, Plebani M, Lippi G", "date": "2020-04-15", "evidence": [], "reference": [ { "id": "32286245", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32286245" } ] }, { "title": "Dysregulation of Immune Response in Patients With Coronavirus 2019 (COVID-19) in Wuhan, China.", "journal": "Clinical infectious diseases : an official publication of the Infectious Diseases Society of America", "authors": "Qin C, Zhou L, Hu Z, Zhang S, Yang S, Tao Y, Xie C, Ma K, Shang K, Wang W, Tian DS", "date": "2020-03-13", "evidence": [], "reference": [ { "id": "32161940", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32161940" } ] }, { "title": "Clinical and epidemiological features of 36 children with coronavirus disease 2019 (COVID-19) in Zhejiang, China: an observational cohort study.", "journal": "The Lancet. Infectious diseases", "authors": "Qiu H, Wu J, Hong L, Luo Y, Song Q, Chen D", "date": "2020-03-30", "evidence": [], "reference": [ { "id": "32220650", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32220650" } ] }, { "title": "Clinical characteristics of 140 patients infected with SARS-CoV-2 in Wuhan, China.", "journal": "Allergy", "authors": "Zhang JJ, Dong X, Cao YY, Yuan YD, Yang YB, Yan YQ, Akdis CA, Gao YD", "date": "2020-02-23", "evidence": [], "reference": [ { "id": "32077115", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32077115" } ] }, { "title": "Lymphopenia is associated with severe coronavirus disease 2019 (COVID-19) infections: A systemic review and meta-analysis.", "journal": "International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases", "authors": "Zhao Q, Meng M, Kumar R, Wu Y, Huang J, Deng Y, Weng Z, Yang L", "date": "2020-05-08", "evidence": [], "reference": [ { "id": "32376308", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32376308" } ] }, { "title": "Biochemical biomarkers alterations in Coronavirus Disease 2019 (COVID-19).", "journal": "Diagnosis (Berlin, Germany)", "authors": "Ciaccio M, Agnello L", "date": "2020-06-27", "evidence": [], "reference": [ { "id": "32589600", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32589600" } ] }, { "title": "Covid-19 infection in therapy-naive patients with B-cell chronic lymphocytic leukemia.", "journal": "Leukemia research", "authors": "Paneesha S, Pratt G, Parry H, Moss P", "date": "2020-05-11", "evidence": [], "reference": [ { "id": "32388230", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32388230" } ] } ], "biomarker_canonical_id": "AN6281", "score": 3.8, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 9 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6282-1", "biomarker_component": [ { "biomarker": "decreased LYMP count", "assessed_biomarker_entity": { "recommended_name": "Lymphocyte", "synonyms": [] }, "assessed_biomarker_entity_id": "CO:CL_0000542", "assessed_entity_type": "cell", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "21448592", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/21448592", "evidence_list": [ { "evidence": "Lymphopenia was found in 49/260 (19%) of patients. Ten of these 49 patients had severe hematological toxicity. Lymphopenia was strongly associated with shorter progression-free survival (median 4 vs. 7 months; P = 0.033) and shorter overall survival (median 16 vs. 24 months, P = 0.024). Multivariate analysis revealed that lymphopenia had an independent effect on survival. Lymphopenia in conclusion is proven to be an independent predictive factor for chemotherapy and hematological toxicity in colorectal cancer." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_9256" }, "synonyms": [] }, "evidence_source": [ { "id": "21448592", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/21448592", "evidence_list": [ { "evidence": "Lymphopenia was found in 49/260 (19%) of patients. Ten of these 49 patients had severe hematological toxicity. Lymphopenia was strongly associated with shorter progression-free survival (median 4 vs. 7 months; P = 0.033) and shorter overall survival (median 16 vs. 24 months, P = 0.024). Multivariate analysis revealed that lymphopenia had an independent effect on survival. Lymphopenia in conclusion is proven to be an independent predictive factor for chemotherapy and hematological toxicity in colorectal cancer." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Pre-treatment lymphopenia as a prognostic biomarker in colorectal cancer patients receiving chemotherapy.", "journal": "Cancer chemotherapy and pharmacology", "authors": "Cézé N, Thibault G, Goujon G, Viguier J, Watier H, Dorval E, Lecomte T", "date": "2011-03-31", "evidence": [], "reference": [ { "id": "21448592", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/21448592" } ] } ], "biomarker_canonical_id": "AN6282", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "c": "condition", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6282-2", "biomarker_component": [ { "biomarker": "decreased LYMP count", "assessed_biomarker_entity": { "recommended_name": "Lymphocyte", "synonyms": [] }, "assessed_biomarker_entity_id": "CO:CL_0000542", "assessed_entity_type": "cell", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "19549917", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/19549917", "evidence_list": [ { "evidence": "In multivariate analysis (Cox model), lymphopenia was an independent prognostic factor for overall survival in metastatic breast cancer (RR: 1.8; 95%CI 1.3-2.4) along with liver metastases and PS; in advanced soft-tissue sarcoma (RR: 1.46; 95%CI 1.0-2.1) along with liver metastases, lung metastases and PS; and in non-Hodgkin‚Äôs lymphoma (RR: 1.48; 95%CI 1.03-2.1) along with IPI. Our findings demonstrate that lymphopenia is an independent prognostic factor for overall and progression-free survival in several cancers." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "name": "breast cancer", "description": "A thoracic cancer that originates in the mammary gland.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, "synonyms": [ { "id": "DOID:1612", "name": "malignant tumor of the breast", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "breast tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "mammary cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "primary breast cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "mammary tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "malignant neoplasm of breast", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" } ] }, "evidence_source": [ { "id": "19549917", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/19549917", "evidence_list": [ { "evidence": "In multivariate analysis (Cox model), lymphopenia was an independent prognostic factor for overall survival in metastatic breast cancer (RR: 1.8; 95%CI 1.3-2.4) along with liver metastases and PS; in advanced soft-tissue sarcoma (RR: 1.46; 95%CI 1.0-2.1) along with liver metastases, lung metastases and PS; and in non-Hodgkin‚Äôs lymphoma (RR: 1.48; 95%CI 1.03-2.1) along with IPI. Our findings demonstrate that lymphopenia is an independent prognostic factor for overall and progression-free survival in several cancers." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Lymphopenia as a prognostic factor for overall survival in advanced carcinomas, sarcomas, and lymphomas.", "journal": "Cancer research", "authors": "Ray-Coquard I, Cropet C, Van Glabbeke M, Sebban C, Le Cesne A, Judson I, Tredan O, Verweij J, Biron P, Labidi I, Guastalla JP, Bachelot T, Perol D, Chabaud S, Hogendoorn PC, Cassier P, Dufresne A, Blay JY, None None", "date": "2009-06-25", "evidence": [], "reference": [ { "id": "19549917", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/19549917" } ] } ], "biomarker_canonical_id": "AN6282", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, 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"specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:9351", "recommended_name": { "id": "DOID:9351", "name": "diabetes mellitus", "description": "A glucose metabolism disease that is characterized by chronic hyperglycaemia with disturbances of carbohydrate, fat and protein metabolism resulting from defects in insulin secretion, insulin action, or both.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_9351" }, "synonyms": [ { "id": "DOID:9351", "name": "diabetes", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_9351" } ] }, "evidence_source": [ { "id": "15225139", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/15225139", "evidence_list": [ { "evidence": "In the present study, the number of leukocytes was increased but that of lymphocytes was decreased in diabetic patients." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Diabetes induces apoptosis in lymphocytes.", "journal": "The Journal of endocrinology", "authors": "Otton R, Soriano FG, Verlengia R, Curi R", "date": "2004-07-01", "evidence": [], "reference": [ { "id": "15225139", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/15225139" } ] } ], "biomarker_canonical_id": "AN6282", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "c": "condition", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6283-1", "biomarker_component": [ { "biomarker": "decreased PLAT count", "assessed_biomarker_entity": { "recommended_name": "Platelet", "synonyms": [ { "synonym": "anucleate thrombocyte" }, { "synonym": "blood 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"https://pubmed.ncbi.nlm.nih.gov/32286245", "evidence_list": [ { "evidence": "In hospitalized patients with respiratory distress, we recommend clinicians closely monitor WBC count, lymphocyte count, platelet count, IL-6 and serum ferritin as markers for potential progression to critical illness." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32475810", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32475810", "evidence_list": [ { "evidence": "Meta-analysis of 1799 patients reveal those with severe COVID-19 infections had significantly lower platelet counts. Despite the varying definitions of disease severity and thrombocytopenia having an influence on results analysis, platelet count could possibly be used clinically to indicate infection severity. Lymphocytes and platelet count showed significantly lower levels in severe patients compared to non-severe patients." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32352397", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32352397", "evidence_list": [ { "evidence": "In this study, the most important finding was that the neutrophil count, lymphocyte count and platelet count were independent risk factors for predicting the development of severe illness in COVID-19 patients." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] }, { "biomarker": "Decreased platelet level", "assessed_biomarker_entity": { "recommended_name": "Thrombocytopenia", "synonyms": [ { "synonym": "anucleate thrombocyte" }, { "synonym": "blood platelet" }, { "synonym": "enucleate thrombocyte" } ] }, "assessed_biomarker_entity_id": "CO:CL_0000233", "assessed_entity_type": "cell", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "2157-6" } ], "evidence_source": [ { "id": "32589600", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32589600", "evidence_list": [ { "evidence": "Many biomarkers have been associated with poor outcomes and represent a candidate for risk stratification models for predicting severe COVID-19 in order to guide clinical care. Among all, lymphopenia, thrombocytopenia, leucocytosis, CRP, PCT, LDH, AST, ALT, D-dimer, cTn represent the most predictive parameters of severe COVID-19" } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:0080600", "recommended_name": { "id": "DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, "synonyms": [ { "id": "DOID:0080600", "name": "SARS-CoV-2 infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan coronavirus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "COVID19", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan seafood market pneumonia virus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019-nCoV infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019 Novel Coronavirus (2019-nCoV)", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" } ] }, "evidence_source": [ { "id": "32178975", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32178975", "evidence_list": [ { "evidence": "Low platelet count is associated with increased risk of severe disease and mortality in patients with COVID-19, and thus should serve as clinical indicator of worsening illness during hospitalization." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32286245", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32286245", "evidence_list": [ { "evidence": "In hospitalized patients with respiratory distress, we recommend clinicians closely monitor WBC count, lymphocyte count, platelet count, IL-6 and serum ferritin as markers for potential progression to critical illness." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32475810", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32475810", "evidence_list": [ { "evidence": "Meta-analysis of 1799 patients reveal those with severe COVID-19 infections had significantly lower platelet counts. Despite the varying definitions of disease severity and thrombocytopenia having an influence on results analysis, platelet count could possibly be used clinically to indicate infection severity. Lymphocytes and platelet count showed significantly lower levels in severe patients compared to non-severe patients." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32352397", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32352397", "evidence_list": [ { "evidence": "In this study, the most important finding was that the neutrophil count, lymphocyte count and platelet count were independent risk factors for predicting the development of severe illness in COVID-19 patients." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32589600", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32589600", "evidence_list": [ { "evidence": "Many biomarkers have been associated with poor outcomes and represent a candidate for risk stratification models for predicting severe COVID-19 in order to guide clinical care. Among all, lymphopenia, thrombocytopenia, leucocytosis, CRP, PCT, LDH, AST, ALT, D-dimer, cTn represent the most predictive parameters of severe COVID-19" } ], "tags": [ { "tag": "condition" }, { "tag": "best_biomarker_role" } ] } ], "citation": [ { "title": "Thrombocytopenia is associated with severe coronavirus disease 2019 (COVID-19) infections: A meta-analysis.", "journal": "Clinica chimica acta; international journal of clinical chemistry", "authors": "Lippi G, Plebani M, Henry BM", "date": "2020-03-18", "evidence": [], "reference": [ { "id": "32178975", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32178975" } ] }, { "title": "Hematologic, biochemical and immune biomarker abnormalities associated with severe illness and mortality in coronavirus disease 2019 (COVID-19): a meta-analysis.", "journal": "Clinical chemistry and laboratory medicine", "authors": "Henry BM, de Oliveira MHS, Benoit S, Plebani M, Lippi G", "date": "2020-04-15", "evidence": [], "reference": [ { "id": "32286245", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32286245" } ] }, { "title": "The role of biomarkers in diagnosis of COVID-19 - A systematic review.", "journal": "Life sciences", "authors": "Kermali M, Khalsa RK, Pillai K, Ismail Z, Harky A", "date": "2020-06-02", "evidence": [], "reference": [ { "id": "32475810", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32475810" } ] }, { "title": "The hemocyte counts as a potential biomarker for predicting disease progression in COVID-19: a retrospective study.", "journal": "Clinical chemistry and laboratory medicine", "authors": "Zheng Y, Zhang Y, Chi H, Chen S, Peng M, Luo L, Chen L, Li J, Shen B, Wang D", "date": "2020-05-01", "evidence": [], "reference": [ { "id": "32352397", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32352397" } ] }, { "title": "Biochemical biomarkers alterations in Coronavirus Disease 2019 (COVID-19).", "journal": "Diagnosis (Berlin, Germany)", "authors": "Ciaccio M, Agnello L", "date": "2020-06-27", "evidence": [], "reference": [ { "id": "32589600", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32589600" } ] } ], "biomarker_canonical_id": "AN6283", "score": 2.8, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 4 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "c": "condition", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6284-1", "biomarker_component": [ { "biomarker": "increased SFER level", "assessed_biomarker_entity": { "recommended_name": "Serum ferritin", "synonyms": [] }, "assessed_biomarker_entity_id": "PRO:PR_000050342", "assessed_entity_type": "protein complex", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": 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"tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Hematologic, biochemical and immune biomarker abnormalities associated with severe illness and mortality in coronavirus disease 2019 (COVID-19): a meta-analysis.", "journal": "Clinical chemistry and laboratory medicine", "authors": "Henry BM, de Oliveira MHS, Benoit S, Plebani M, Lippi G", "date": "2020-04-15", "evidence": [], "reference": [ { "id": "32286245", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32286245" } ] }, { "title": "Hematological findings and complications of COVID-19.", "journal": "American journal of hematology", "authors": "Terpos E, Ntanasis-Stathopoulos I, Elalamy I, Kastritis E, Sergentanis TN, Politou M, Psaltopoulou T, Gerotziafas G, Dimopoulos MA", "date": "2020-04-14", "evidence": [], "reference": [ { "id": "32282949", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32282949" } ] } ], "biomarker_canonical_id": "AN6284", "score": 2.2, 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Higher CD4 levels predicted improved overall and disease specific survival (p=.003 and .004 respectively)." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0001729" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:11934", "recommended_name": { "id": "DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11934" }, "synonyms": [ { "id": "DOID:11934", "name": "head and neck neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11934" }, { "id": "DOID:11934", "name": "head/neck neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11934" }, { "id": "DOID:11934", "name": "head and neck tumours", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11934" }, { "id": "DOID:11934", "name": "tumor of head and neck", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11934" } ] }, "evidence_source": [ { "id": "26879675", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/26879675", "evidence_list": [ { "evidence": "Higher CD4 and CD8 TIL levels were associated with improved overall (HR 0.77 [0.65 ‚Äì0.93] p=.005 and HR 0.77 [0.64‚Äì0.94] p=.008 respectively), and relapse free survival (p=.03, and .05 respectively). Higher CD4 levels predicted improved overall and disease specific survival (p=.003 and .004 respectively)." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Tumor infiltrating lymphocytes and survival in patients with head and neck squamous cell carcinoma.", "journal": "Head & neck", "authors": "Nguyen N, Bellile E, Thomas D, McHugh J, Rozek L, Virani S, Peterson L, Carey TE, Walline H, Moyer J, Spector M, Perim D, Prince M, McLean S, Bradford CR, Taylor JM, Wolf GT, None None", "date": "2016-02-18", "evidence": [], "reference": [ { "id": "26879675", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/26879675" } ] } ], "biomarker_canonical_id": "AN6288", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "f": "frequency", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6290-5", "biomarker_component": [ { "biomarker": "increased CRP level", "assessed_biomarker_entity": { "recommended_name": "C-reactive protein", "synonyms": [] }, "assessed_biomarker_entity_id": "UPKB:P02741", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "71426-1" } ], "evidence_source": [ { "id": "32277967", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32277967", "evidence_list": [ { "evidence": "SAA/L, CRP, SAA, and L count are valuable in predicting the severity and distinguishing critically ill patients from mild ones." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32677844", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32677844", "evidence_list": [ { "evidence": "Elevated levels of IL-6, D-dimer, CRP, LDH, and ferritin all had an independent increased risk for the clinical outcomes assessed (ICU admission, invasive ventilatory support and death), which were statistically significant." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32347972", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32347972", "evidence_list": [ { "evidence": "The positive correlations between CRP and series cancer biomarkers we showed in this study demonstrate that these cancer biomarkers can present the diffuse and acute lung injuries in COVID-19. CRP increased in 95% of all cases; the increases were significant for all groups (mild: 13.5‚Ä⬱‚Äâ13.1; severe: 35.0‚Ä⬱‚Äâ39.2; critical: 66.1‚Ä⬱‚Äâ67.3; in mg/L; P‚Äâ=‚Äâ.002)." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "33349241", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/33349241", "evidence_list": [ { "evidence": "Biomarkers that predict the mortality of individual patients more than 10 days in advance with more than 90% accuracy: lactic dehydrogenase (LDH), lymphocyte and high-sensitivity C-reactive protein (hs-CRP). [DOI:10.1038/s42256-020-0180-7] With following parameters such as age >67.5 years, IL2R >793.5U/mL, CRP >30.7ng/mL, ferroprotein >2252ug/L, WBC>9.5x10^9/L or NC >7.305x10^9/L, the progress of COVID-19 to critical stage should be closely observed and possibly prevented." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32161940", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32161940", "evidence_list": [ { "evidence": "Surveillance of NLR and lymphocyte subsets is helpful in the early screening of critical illness, diagnosis, and treatment of COVID-19." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32425269", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32425269", "evidence_list": [ { "evidence": "The maximal level of IL-6, followed by CRP level, was highly predictive of the need for mechanical ventilation. This suggests the possibility of using IL-6 or CRP level to guide escalation of treatment in patients with COVID-19-related hyperinflammatory syndrome." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32566572", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32566572", "evidence_list": [ { "evidence": "NLR and CRP are potential and reliable predictors of COVID-19 prognosis and can triage patients at the time of admission." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32243911", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32243911", "evidence_list": [ { "evidence": "At the early stage of COVID-19, CRP levels were positively correlated with lung lesions. CRP levels could reflect disease severity and should be used as a key indicator for disease monitoring." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32475810", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32475810", "evidence_list": [ { "evidence": "C-reactive protein, serum amyloid A, interleukin-6, lactate dehydrogenase, neutrophil-to-lymphocyte ratio, D-dimer, cardiac troponin, and renal biomarkers showed significantly higher levels in patients with severe complications of COVID-19 infection compared to their non-severe counterparts." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32296824", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32296824", "evidence_list": [ { "evidence": "We found that old age, and higher serum lactate dehydrogenase, C-reactive protein, the coefficient of variation of red blood cell distribution width, blood urea nitrogen, direct bilirubin, lower albumin, are associated with severe COVID-19." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32281668", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32281668", "evidence_list": [ { "evidence": "CRP changes before other blood parameters and thus may be an effective evaluation index for patients with COVID-19 infection. [DOI:10.1101/2020.03.10.20033613] CRP in severe COVID-19 patients increased significantly at the initial stage, before CT findings. Importantly, CRP, which was associated with disease development, predicted early severe COVID-19." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32368728", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32368728", "evidence_list": [ { "evidence": "The combination of eosinopenia and elevated hs-CRP can effectively triage suspected COVID-19 patients from other patients attending the fever clinic with COVID-19-like initial symptoms." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32277967", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32277967", "evidence_list": [ { "evidence": "Patients with higher initial SAA are more likely to have poor CT imaging. Our study indicated that SAA/L. CRP, SAA, and l are valuable in predicting the severity and distinguishing critically ill patients from mild ones." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32475810", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32475810", "evidence_list": [ { "evidence": "CRP is one of the first biomarkers within blood plasma that changes to reflect physiological complications; if accepted CRP will be the most effective biomarker to predict the progression of COVID-19 infection. CRP values are more reliable for earlier identification of case severity." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32281668", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32281668", "evidence_list": [ { "evidence": "CRP which was associated with disease development, predicted early severe COVID-19." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32511972", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32511972", "evidence_list": [ { "evidence": "Biomarkers that predict the mortality of individual patients more than 10 days in advance with more than 90% accuracy: lactic dehydrogenase (LDH), lymphocyte and high-sensitivity C-reactive protein (hs-CRP). [DOI:10.1038/s42256-020-0180-7] Concentrations of CRP remained high in patients who died of COVID-19 infection, and CRP could be a biomarker for assessing disease lethality." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32344321", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32344321", "evidence_list": [ { "evidence": "The serum levels of IL-6 and CRP can effectively assess disease severity and predict outcome in patients with COVID-19." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32615866", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32615866", "evidence_list": [ { "evidence": "The serum levels of CRP, PCT and ferritin are markedly increased in very severe compared with severe COVID-19." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32471703", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32471703", "evidence_list": [ { "evidence": "We propose that a few parameters, such Lymphocytes count, L/N ratio, SaO2 and CRP serum level can be used to assess the severity of COVID-19 in emergency room." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32414383", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32414383", "evidence_list": [ { "evidence": "The plasma CRP level is positively correlated to the severity of COVID-19 on CT performance, and higher level of CRP showed a longer inpatient duration." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32048163", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32048163", "evidence_list": [ { "evidence": "The combinations of the hypoalbuminemia, lymphopenia, and high concentrations of CRP and LDH in 2019-nCoV infected patients upon hospital admission may predict more severe acute lung injury." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32243911", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32243911", "evidence_list": [ { "evidence": "Best baseline predictors of respiratory failure were suPAR with an AUC (95% CI) of 0.88 (0.80-0.95), EWS 0.84 (0.75-0.93), LDH 0.82 (0.71-0.93), and CRP 0.80 (0.70-0.89. [DOI:10.1101/2020.05.27.20114678] At the early stage of COVID-19, CRP levels were positively cor-related with lung lesions. CRP levels could reflect disease severity and should be used as a key indicator for disease monitoring." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32369209", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32369209", "evidence_list": [ { "evidence": "Our results showed that the laboratory tests of cancer patients had the following characteristics: low lymphocytes, increased IL-6, CRP, PCT, D dimer, and LDH. The increase of these inflammatory indexes indicates that the infected patients were in inflammatory state, which may be closely related to the inflammatory storm." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "monitoring" } ], "condition": { "id": "DOID:0080600", "recommended_name": { "id": "DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, "synonyms": [ { "id": "DOID:0080600", "name": "SARS-CoV-2 infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan coronavirus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "COVID19", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan seafood market pneumonia virus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019-nCoV infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019 Novel Coronavirus (2019-nCoV)", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" } ] }, "evidence_source": [ { "id": "32677844", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32677844", "evidence_list": [ { "evidence": "Elevated levels of IL-6, D-dimer, CRP, LDH, and ferritin all had an independent increased risk for the clinical outcomes assessed (ICU admission, invasive ventilatory support and death), which were statistically significant." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32347972", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32347972", "evidence_list": [ { "evidence": "The positive correlations between CRP and series cancer biomarkers we showed in this study demonstrate that these cancer biomarkers can present the diffuse and acute lung injuries in COVID-19. CRP increased in 95% of all cases; the increases were significant for all groups (mild: 13.5‚Ä⬱‚Äâ13.1; severe: 35.0‚Ä⬱‚Äâ39.2; critical: 66.1‚Ä⬱‚Äâ67.3; in mg/L; P‚Äâ=‚Äâ.002)." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "33349241", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/33349241", "evidence_list": [ { "evidence": "Biomarkers that predict the mortality of individual patients more than 10 days in advance with more than 90% accuracy: lactic dehydrogenase (LDH), lymphocyte and high-sensitivity C-reactive protein (hs-CRP). [DOI:10.1038/s42256-020-0180-7] With following parameters such as age >67.5 years, IL2R >793.5U/mL, CRP >30.7ng/mL, ferroprotein >2252ug/L, WBC>9.5x10^9/L or NC >7.305x10^9/L, the progress of COVID-19 to critical stage should be closely observed and possibly prevented." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32161940", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32161940", "evidence_list": [ { "evidence": "Surveillance of NLR and lymphocyte subsets is helpful in the early screening of critical illness, diagnosis, and treatment of COVID-19." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32425269", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32425269", "evidence_list": [ { "evidence": "The maximal level of IL-6, followed by CRP level, was highly predictive of the need for mechanical ventilation. This suggests the possibility of using IL-6 or CRP level to guide escalation of treatment in patients with COVID-19-related hyperinflammatory syndrome." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32566572", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32566572", "evidence_list": [ { "evidence": "NLR and CRP are potential and reliable predictors of COVID-19 prognosis and can triage patients at the time of admission." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32296824", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32296824", "evidence_list": [ { "evidence": "We found that old age, and higher serum lactate dehydrogenase, C-reactive protein, the coefficient of variation of red blood cell distribution width, blood urea nitrogen, direct bilirubin, lower albumin, are associated with severe COVID-19." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32368728", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32368728", "evidence_list": [ { "evidence": "The combination of eosinopenia and elevated hs-CRP can effectively triage suspected COVID-19 patients from other patients attending the fever clinic with COVID-19-like initial symptoms." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32511972", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32511972", "evidence_list": [ { "evidence": "Biomarkers that predict the mortality of individual patients more than 10 days in advance with more than 90% accuracy: lactic dehydrogenase (LDH), lymphocyte and high-sensitivity C-reactive protein (hs-CRP). [DOI:10.1038/s42256-020-0180-7] Concentrations of CRP remained high in patients who died of COVID-19 infection, and CRP could be a biomarker for assessing disease lethality." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32344321", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32344321", "evidence_list": [ { "evidence": "The serum levels of IL-6 and CRP can effectively assess disease severity and predict outcome in patients with COVID-19." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32615866", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32615866", "evidence_list": [ { "evidence": "The serum levels of CRP, PCT and ferritin are markedly increased in very severe compared with severe COVID-19." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32471703", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32471703", "evidence_list": [ { "evidence": "We propose that a few parameters, such Lymphocytes count, L/N ratio, SaO2 and CRP serum level can be used to assess the severity of COVID-19 in emergency room." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32414383", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32414383", "evidence_list": [ { "evidence": "The plasma CRP level is positively correlated to the severity of COVID-19 on CT performance, and higher level of CRP showed a longer inpatient duration." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32048163", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32048163", "evidence_list": [ { "evidence": "The combinations of the hypoalbuminemia, lymphopenia, and high concentrations of CRP and LDH in 2019-nCoV infected patients upon hospital admission may predict more severe acute lung injury." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32369209", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32369209", "evidence_list": [ { "evidence": "Our results showed that the laboratory tests of cancer patients had the following characteristics: low lymphocytes, increased IL-6, CRP, PCT, D dimer, and LDH. The increase of these inflammatory indexes indicates that the infected patients were in inflammatory state, which may be closely related to the inflammatory storm." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32259132", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32259132", "evidence_list": [ { "evidence": "Our findings suggest that level of LDH, CRP, ALT and NEU can be used to predict the result of COVID-19 test." } ], "tags": [ { "tag": "condition" }, { "tag": "best_biomarker_role" } ] }, { "id": "32503382", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32503382", "evidence_list": [ { "evidence": "Erythrocyte sedimentation rate (ESR) (R=0.55, p < .01) was positively associated with CT severity scores. To sum up, we can conclude from the analysis of published studies that hematological (lymphocyte count, neutrophil count, and NLR), inflammatory (CRP, ESR, IL-6), and especially biochemical (D-dimer, Troponins, CK) parameters correlate with severe prognosis or exitus in COVID-19 patients and can therefore be used as predictive biomarkers." } ], "tags": [ { "tag": "condition" }, { "tag": "best_biomarker_role" } ] }, { "id": "32324595", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32324595", "evidence_list": [ { "evidence": "Inflammatory biomarkers such as CRP and erythrocyte sedimentation rate were increased." } ], "tags": [ { "tag": "condition" }, { "tag": "best_biomarker_role" } ] }, { "id": "32669866", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32669866", "evidence_list": [ { "evidence": "The measurement of CRP was increased by 79.93% in all patients." } ], "tags": [ { "tag": "condition" }, { "tag": "best_biomarker_role" } ] }, { "id": "32492406", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32492406", "evidence_list": [ { "evidence": "Compared to non-severe patients, severe patients showed significant suppression of lymphocyte count and monocyte count, as well as increase of CRP and AST." } ], "tags": [ { "tag": "condition" }, { "tag": "best_biomarker_role" } ] }, { "id": "32589600", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32589600", "evidence_list": [ { "evidence": "Many biomarkers have been associated with poor outcomes and represent a candidate for risk stratification models for predicting severe COVID-19 in order to guide clinical care. Among all, lymphopenia, thrombocytopenia, leucocytosis, CRP, PCT, LDH, AST, ALT, D-dimer, cTn represent the most predictive parameters of severe COVID-19" } ], "tags": [ { "tag": "condition" }, { "tag": "best_biomarker_role" } ] }, { "id": "32766546", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32766546", "evidence_list": [ { "evidence": "On multivariable analysis, the risk factors found to be significantly associated with admission to intensive care were age above 50 years old, a qSOFA score above 0, smoking, elevated CRP and elevated procalcitonin levels. Asthma, smoking and elevated procalcitonin levels correlated significantly with mortality in our cohort." } ], "tags": [ { "tag": "condition" }, { "tag": "best_biomarker_role" } ] }, { "id": "32388230", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32388230", "evidence_list": [ { "evidence": "Patient 1: CRP level peaked at 332 mg/L.Patient 2: CRP level was 368 mg/L.Patient 3: CRP level was 396 mg/L." } ], "tags": [ { "tag": "condition" }, { "tag": "best_biomarker_role" } ] } ], "citation": [ { "title": "Serum Amyloid A is a biomarker of severe Coronavirus Disease and poor prognosis.", "journal": "The Journal of infection", "authors": "Li H, Xiang X, Ren H, Xu L, Zhao L, Chen X, Long H, Wang Q, Wu Q", "date": "2020-04-12", "evidence": [], "reference": [ { "id": "32277967", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32277967" } ] }, { "title": "The association between biomarkers and clinical outcomes in novel coronavirus pneumonia in a US cohort.", "journal": "Biomarkers in medicine", "authors": "Ayanian S, Reyes J, Lynn L, Teufel K", "date": "2020-07-18", "evidence": [], "reference": [ { "id": "32677844", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32677844" } ] }, { "title": "Elevations of serum cancer biomarkers correlate with severity of COVID-19.", "journal": "Journal of medical virology", "authors": "Wei X, Su J, Yang K, Wei J, Wan H, Cao X, Tan W, Wang H", "date": "2020-04-30", "evidence": [], "reference": [ { "id": "32347972", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32347972" } ] }, { "title": "Correlation analysis between disease severity and inflammation-related parameters in patients with COVID-19: a retrospective study.", "journal": "BMC infectious diseases", "authors": "Gong J, Dong H, Xia QS, Huang ZY, Wang DK, Zhao Y, Liu WH, Tu SH, Zhang MM, Wang Q, Lu FE", "date": "2020-12-23", "evidence": [], "reference": [ { "id": "33349241", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/33349241" } ] }, { "title": "Dysregulation of Immune Response in Patients With Coronavirus 2019 (COVID-19) in Wuhan, China.", "journal": "Clinical infectious diseases : an official publication of the Infectious Diseases Society of America", "authors": "Qin C, Zhou L, Hu Z, Zhang S, Yang S, Tao Y, Xie C, Ma K, Shang K, Wang W, Tian DS", "date": "2020-03-13", "evidence": [], "reference": [ { "id": "32161940", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32161940" } ] }, { "title": "Elevated levels of IL-6 and CRP predict the need for mechanical ventilation in COVID-19.", "journal": "The Journal of allergy and clinical immunology", "authors": "Herold T, Jurinovic V, Arnreich C, Lipworth BJ, Hellmuth JC, von Bergwelt-Baildon M, Klein M, Weinberger T", "date": "2020-05-20", "evidence": [], "reference": [ { "id": "32425269", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32425269" } ] }, { "title": "Combined use of the neutrophil-to-lymphocyte ratio and CRP to predict 7-day disease severity in 84 hospitalized patients with COVID-19 pneumonia: a retrospective cohort study.", "journal": "Annals of translational medicine", "authors": "Liu YP, Li GM, He J, Liu Y, Li M, Zhang R, Li YL, Wu YZ, Diao B", "date": "2020-06-23", "evidence": [], "reference": [ { "id": "32566572", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32566572" } ] }, { "title": "C-reactive protein levels in the early stage of COVID-19.", "journal": "Medecine et maladies infectieuses", "authors": "Wang L", "date": "2020-04-04", "evidence": [], "reference": [ { "id": "32243911", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32243911" } ] }, { "title": "The role of biomarkers in diagnosis of COVID-19 - A systematic review.", "journal": "Life sciences", "authors": "Kermali M, Khalsa RK, Pillai K, Ismail Z, Harky A", "date": "2020-06-02", "evidence": [], "reference": [ { "id": "32475810", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32475810" } ] }, { "title": "A Tool for Early Prediction of Severe Coronavirus Disease 2019 (COVID-19): A Multicenter Study Using the Risk Nomogram in Wuhan and Guangdong, China.", "journal": "Clinical infectious diseases : an official publication of the Infectious Diseases Society of America", "authors": "Gong J, Ou J, Qiu X, Jie Y, Chen Y, Yuan L, Cao J, Tan M, Xu W, Zheng F, Shi Y, Hu B", "date": "2020-04-17", "evidence": [], "reference": [ { "id": "32296824", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32296824" } ] }, { "title": "C-reactive protein correlates with computed tomographic findings and predicts severe COVID-19 early.", "journal": "Journal of medical virology", "authors": "Tan C, Huang Y, Shi F, Tan K, Ma Q, Chen Y, Jiang X, Li X", "date": "2020-04-14", "evidence": [], "reference": [ { "id": "32281668", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32281668" } ] }, { "title": "Eosinopenia and elevated C-reactive protein facilitate triage of COVID-19 patients in fever clinic: A retrospective case-control study.", "journal": "EClinicalMedicine", "authors": "Li Q, Ding X, Xia G, Chen HG, Chen F, Geng Z, Xu L, Lei S, Pan A, Wang L, Wang Z", "date": "2020-05-06", "evidence": [], "reference": [ { "id": "32368728", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32368728" } ] }, { "title": "C-reactive protein: A promising biomarker for poor prognosis in COVID-19 infection.", "journal": "Clinica chimica acta; international journal of clinical chemistry", "authors": "Sahu BR, Kampa RK, Padhi A, Panda AK", "date": "2020-06-09", "evidence": [], "reference": [ { "id": "32511972", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32511972" } ] }, { "title": "Prognostic value of interleukin-6, C-reactive protein, and procalcitonin in patients with COVID-19.", "journal": "Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology", "authors": "Liu F, Li L, Xu M, Wu J, Luo D, Zhu Y, Li B, Song X, Zhou X", "date": "2020-04-29", "evidence": [], "reference": [ { "id": "32344321", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32344321" } ] }, { "title": "C-reactive protein, procalcitonin, D-dimer, and ferritin in severe coronavirus disease-2019: a meta-analysis.", "journal": "Therapeutic advances in respiratory disease", "authors": "Huang I, Pranata R, Lim MA, Oehadian A, Alisjahbana B", "date": "2020-07-04", "evidence": [], "reference": [ { "id": "32615866", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32615866" } ] }, { "title": "Laboratory Biomarkers Predicting COVID-19 Severity in the Emergency Room.", "journal": "Archives of medical research", "authors": "Assandri R, Buscarini E, Canetta C, Scartabellati A, Viganò G, Montanelli A", "date": "2020-05-31", "evidence": [], "reference": [ { "id": "32471703", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32471703" } ] }, { "title": "Plasma CRP level is positively associated with the severity of COVID-19.", "journal": "Annals of clinical microbiology and antimicrobials", "authors": "Chen W, Zheng KI, Liu S, Yan Z, Xu C, Qiao Z", "date": "2020-05-18", "evidence": [], "reference": [ { "id": "32414383", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32414383" } ] }, { "title": "Clinical and biochemical indexes from 2019-nCoV infected patients linked to viral loads and lung injury.", "journal": "Science China. Life sciences", "authors": "Liu Y, Yang Y, Zhang C, Huang F, Wang F, Yuan J, Wang Z, Li J, Li J, Feng C, Zhang Z, Wang L, Peng L, Chen L, Qin Y, Zhao D, Tan S, Yin L, Xu J, Zhou C, Jiang C, Liu L", "date": "2020-02-13", "evidence": [], "reference": [ { "id": "32048163", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32048163" } ] }, { "title": "Clinical characteristics and outcomes of cancer patients with COVID-19.", "journal": "Journal of medical virology", "authors": "Yang F, Shi S, Zhu J, Shi J, Dai K, Chen X", "date": "2020-05-06", "evidence": [], "reference": [ { "id": "32369209", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32369209" } ] }, { "title": "Laboratory Parameters in Detection of COVID-19 Patients with Positive RT-PCR; a Diagnostic Accuracy Study.", "journal": "Archives of academic emergency medicine", "authors": "Mardani R, Ahmadi Vasmehjani A, Zali F, Gholami A, Mousavi Nasab SD, Kaghazian H, Kaviani M, Ahmadi N", "date": "2020-04-08", "evidence": [], "reference": [ { "id": "32259132", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32259132" } ] }, { "title": "Biomarkers associated with COVID-19 disease progression.", "journal": "Critical reviews in clinical laboratory sciences", "authors": "Ponti G, Maccaferri M, Ruini C, Tomasi A, Ozben T", "date": "2020-06-07", "evidence": [], "reference": [ { "id": "32503382", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32503382" } ] }, { "title": "The laboratory tests and host immunity of COVID-19 patients with different severity of illness.", "journal": "JCI insight", "authors": "Wang F, Hou H, Luo Y, Tang G, Wu S, Huang M, Liu W, Zhu Y, Lin Q, Mao L, Fang M, Zhang H, Sun Z", "date": "2020-04-24", "evidence": [], "reference": [ { "id": "32324595", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32324595" } ] }, { "title": "Alteration of Liver Biomarkers in Patients with SARS-CoV-2 (COVID-19).", "journal": "Journal of inflammation research", "authors": "Gholizadeh P, Safari R, Marofi P, Zeinalzadeh E, Pagliano P, Ganbarov K, Esposito S, Khodadadi E, Yousefi M, Samadi Kafil H", "date": "2020-07-17", "evidence": [], "reference": [ { "id": "32669866", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32669866" } ] }, { "title": "Proteomic and Metabolomic Characterization of COVID-19 Patient Sera.", "journal": "Cell", "authors": "Shen B, Yi X, Sun Y, Bi X, Du J, Zhang C, Quan S, Zhang F, Sun R, Qian L, Ge W, Liu W, Liang S, Chen H, Zhang Y, Li J, Xu J, He Z, Chen B, Wang J, Yan H, Zheng Y, Wang D, Zhu J, Kong Z, Kang Z, Liang X, Ding X, Ruan G, Xiang N, Cai X, Gao H, Li L, Li S, Xiao Q, Lu T, Zhu Y, Liu H, Chen H, Guo T", "date": "2020-06-04", "evidence": [], "reference": [ { "id": "32492406", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32492406" } ] }, { "title": "Biochemical biomarkers alterations in Coronavirus Disease 2019 (COVID-19).", "journal": "Diagnosis (Berlin, Germany)", "authors": "Ciaccio M, Agnello L", "date": "2020-06-27", "evidence": [], "reference": [ { "id": "32589600", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32589600" } ] }, { "title": "Characteristics, risk factors and outcomes among the first consecutive 1096 patients diagnosed with COVID-19 in Kuwait.", "journal": "EClinicalMedicine", "authors": "Almazeedi S, Al-Youha S, Jamal MH, Al-Haddad M, Al-Muhaini A, Al-Ghimlas F, Al-Sabah S", "date": "2020-08-09", "evidence": [], "reference": [ { "id": "32766546", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32766546" } ] }, { "title": "Covid-19 infection in therapy-naive patients with B-cell chronic lymphocytic leukemia.", "journal": "Leukemia research", "authors": "Paneesha S, Pratt G, Parry H, Moss P", "date": "2020-05-11", "evidence": [], "reference": [ { "id": "32388230", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32388230" } ] } ], "biomarker_canonical_id": "AN6290", "score": 3.8, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 9 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "f": "frequency", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6290-1", "biomarker_component": [ { "biomarker": "increased CRP level", "assessed_biomarker_entity": { "recommended_name": "C-reactive protein", "synonyms": [] }, "assessed_biomarker_entity_id": "UPKB:P02741", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "71426-1" } ], "evidence_source": [ { "id": "24481866", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/24481866", "evidence_list": [ { "evidence": "An upregulated TNF-alpha, in combination with CRP, was significantly related to shorter patient survival, independent of clinical stage. Findings indicate that TNF-alpha might be suitable as biomarkers in combination with tumor TNM staging for predicting survival and individualized treatment." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32224151", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32224151", "evidence_list": [ { "evidence": "Highly sensitive C-reactive protein levels in 23 (82.1%) patients. Patients developed severe clinical events; 6 (21.4%) patients were admitted to ICU, 10 (35.7%) patients had life-threatening complications, and 8 (28.6%) of the patients died" } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:11934", "recommended_name": { "id": "DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11934" }, "synonyms": [ { "id": "DOID:11934", "name": "head and neck neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11934" }, { "id": "DOID:11934", "name": "head/neck neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11934" }, { "id": "DOID:11934", "name": "head and neck tumours", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11934" }, { "id": "DOID:11934", "name": "tumor of head and neck", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11934" } ] }, "evidence_source": [ { "id": "24481866", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/24481866", "evidence_list": [ { "evidence": "An upregulated TNF-alpha, in combination with CRP, was significantly related to shorter patient survival, independent of clinical stage. Findings indicate that TNF-alpha might be suitable as biomarkers in combination with tumor TNM staging for predicting survival and individualized treatment." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32224151", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32224151", "evidence_list": [ { "evidence": "Highly sensitive C-reactive protein levels in 23 (82.1%) patients. Patients developed severe clinical events; 6 (21.4%) patients were admitted to ICU, 10 (35.7%) patients had life-threatening complications, and 8 (28.6%) of the patients died" } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Plasma tumor necrosis factor-α and C-reactive protein as biomarker for survival in head and neck squamous cell carcinoma.", "journal": "Journal of cancer research and clinical oncology", "authors": "Andersson BÅ, Lewin F, Lundgren J, Nilsson M, Rutqvist LE, Löfgren S, Laytragoon-Lewin N", "date": "2014-02-01", "evidence": [], "reference": [ { "id": "24481866", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/24481866" } ] }, { "title": "Clinical characteristics of COVID-19-infected cancer patients: a retrospective case study in three hospitals within Wuhan, China.", "journal": "Annals of oncology : official journal of the European Society for Medical Oncology", "authors": "Zhang L, Zhu F, Xie L, Wang C, Wang J, Chen R, Jia P, Guan HQ, Peng L, Chen Y, Peng P, Zhang P, Chu Q, Shen Q, Wang Y, Xu SY, Zhao JP, Zhou M", "date": "2020-04-01", "evidence": [], "reference": [ { "id": "32224151", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32224151" } ] } ], "biomarker_canonical_id": "AN6290", "score": 2.2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 1 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6290-2", "biomarker_component": [ { "biomarker": "increased CRP level", "assessed_biomarker_entity": { "recommended_name": "C-reactive protein", "synonyms": [] }, "assessed_biomarker_entity_id": "UPKB:P02741", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "71426-1" } ], "evidence_source": [ { "id": "19470939", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/19470939", "evidence_list": [ { "evidence": "Elevated SAA and CRP were associated with reduced overall survival, regardless of adjustment for age, tumor stage, race, and body mass index (SAA P trend < .0001; CRP P trend = .002). Elevated CRP (> 3.9 mg/L) showed a statistically significant association with reduced survival; however, HRs were somewhat lower than for SAA. CRP was associated with disease-free survival across all models in a dose-response fashion (P trend = .04 in model 4). Systemic C-reactive protein (CRP) and serum amyloid A (SAA) are measures of low-grade chronic inflammation and potential predictors of cancer survival" } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "name": "breast cancer", "description": "A thoracic cancer that originates in the mammary gland.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, "synonyms": [ { "id": "DOID:1612", "name": "malignant tumor of the breast", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "breast tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "mammary cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "primary breast cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "mammary tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "malignant neoplasm of breast", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" } ] }, "evidence_source": [ { "id": "19470939", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/19470939", "evidence_list": [ { "evidence": "Elevated SAA and CRP were associated with reduced overall survival, regardless of adjustment for age, tumor stage, race, and body mass index (SAA P trend < .0001; CRP P trend = .002). Elevated CRP (> 3.9 mg/L) showed a statistically significant association with reduced survival; however, HRs were somewhat lower than for SAA. CRP was associated with disease-free survival across all models in a dose-response fashion (P trend = .04 in model 4). Systemic C-reactive protein (CRP) and serum amyloid A (SAA) are measures of low-grade chronic inflammation and potential predictors of cancer survival" } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Elevated biomarkers of inflammation are associated with reduced survival among breast cancer patients.", "journal": "Journal of clinical oncology : official journal of the American Society of Clinical Oncology", "authors": "Pierce BL, Ballard-Barbash R, Bernstein L, Baumgartner RN, Neuhouser ML, Wener MH, Baumgartner KB, Gilliland FD, Sorensen BE, McTiernan A, Ulrich CM", "date": "2009-05-28", "evidence": [], "reference": [ { "id": "19470939", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/19470939" } ] } ], "biomarker_canonical_id": "AN6290", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": 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We hypothesize that COVID-19 patients are potentially vulnerable to a significant disease-drug interaction, and therefore, suitable dosing guidelines with therapeutic drug monitoring should be implemented to assure optimal clinical outcomes." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Cytochrome P450-mediated drug interactions in COVID-19 patients: Current findings and possible mechanisms.", "journal": "Medical hypotheses", "authors": "El-Ghiaty MA, Shoieb SM, El-Kadi AOS", "date": "2020-08-08", "evidence": [], "reference": [ { "id": "32758877", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32758877" } ] } ], "biomarker_canonical_id": "AN6292", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "c": "condition", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6293-1", "biomarker_component": [ { "biomarker": "decreased CYP3A4 level", "assessed_biomarker_entity": { "recommended_name": "Cytochrome P450 3A4", "synonyms": [ { "synonym": "1,4-cineole 2-exo-monooxygenase" }, { "synonym": "1,8-cineole 2-exo-monooxygenase" }, { "synonym": "Albendazole monooxygenase (sulfoxide-forming)" }, { "synonym": "Albendazole sulfoxidase" }, { "synonym": "CYPIIIA3" }, { "synonym": "CYPIIIA4" }, { "synonym": "Cholesterol 25-hydroxylase" }, { "synonym": "Cytochrome P450 3A3" }, { "synonym": "Cytochrome P450 HLp" }, { "synonym": "Cytochrome P450 NF-25" }, { "synonym": "Cytochrome P450-PCN1" }, { "synonym": "Nifedipine oxidase" }, { "synonym": "Quinine 3-monooxygenase" } ] }, "assessed_biomarker_entity_id": "UPKB:P08684", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "29109094", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/29109094", "evidence_list": [ { "evidence": "CYP3A4 was identified as a novel tumor suppressor gene related to a poor prognosis in HCC." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:3571", "recommended_name": { "id": "DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, "synonyms": [ { "id": "DOID:3571", "name": "resectable malignant neoplasm of the liver", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "primary liver cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "Resectable malignant neoplasm of Liver", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "neoplasm of liver", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "malignant tumor of liver", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "malignant neoplasm of liver, primary", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "Ca liver - 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A differential protein with m/z 11.6 kDa was detected and identified as an isoform of human serum amyloid A (SAA). It was significantly increased by 1822% in lung cancer patients when compared with the healthy controls, which gave an area under the receiver operator characteristic curve of 0.88. In addition, the protein was also significantly elevated by 77% in lung cancer patients with survival <5 years when compared with patients with survival >/=5 years." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1324" }, "synonyms": [] }, "evidence_source": [ { "id": "20502455", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/20502455", "evidence_list": [ { "evidence": "Study detected increased SAA level in the serum of lung cancer patients and also identified that elevated SAA level may be a non-invasive biomarker useful for the prediction of lung cancer prognosis. A differential protein with m/z 11.6 kDa was detected and identified as an isoform of human serum amyloid A (SAA). It was significantly increased by 1822% in lung cancer patients when compared with the healthy controls, which gave an area under the receiver operator characteristic curve of 0.88. 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IHC revealed diffuse cytoplasmic SAA protein staining in USPC tissues. High intracellular levels of SAA were identified in primary USPC cell lines evaluated by flow cytometry and SAA was found to be actively secreted in vitro." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "monitoring" } ], "condition": { "id": "DOID:1793", "recommended_name": { "id": "DOID:1793", "name": "pancreatic cancer", "description": "An endocrine gland cancer located_in the pancreas.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, "synonyms": [ { "id": "DOID:1793", "name": "Ca head of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "Ca body of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "pancreatic tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "malignant neoplasm of tail of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "malignant neoplasm of head of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "pancreatic neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "Ca tail of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "pancreas neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "malignant neoplasm of body of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" } ] }, "evidence_source": [ { "id": "16211233", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/16211233", "evidence_list": [ { "evidence": "The level of SAA in plasma of pancreatic cancer patients correlated with clinical stage and was significantly higher than in normal volunteers." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "19536090", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/19536090", "evidence_list": [ { "evidence": "SAA gene expression levels were significantly higher in USPC when compared with NEC (mean copy number by RT-PCR=162 vs 2.21; P=0.0002). IHC revealed diffuse cytoplasmic SAA protein staining in USPC tissues. High intracellular levels of SAA were identified in primary USPC cell lines evaluated by flow cytometry and SAA was found to be actively secreted in vitro." } ], "tags": [ { "tag": "condition" }, { "tag": "best_biomarker_role" } ] } ], "citation": [ { "title": "Serum amyloid A as a tumor marker in sera of nude mice with orthotopic human pancreatic cancer and in plasma of patients with pancreatic cancer.", "journal": "International journal of oncology", "authors": "Yokoi K, Shih LC, Kobayashi R, Koomen J, Hawke D, Li D, Hamilton SR, Abbruzzese JL, Coombes KR, Fidler IJ", "date": "2005-10-08", "evidence": [], "reference": [ { "id": "16211233", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/16211233" } ] }, { "title": "Serum amyloid A (SAA): a novel biomarker for uterine serous papillary cancer.", "journal": "British journal of cancer", "authors": "Cocco E, Bellone S, El-Sahwi K, Cargnelutti M, Casagrande F, Buza N, Tavassoli FA, Siegel ER, Visintin I, Ratner E, Silasi DA, Azodi M, Schwartz PE, Rutherford TJ, Pecorelli S, Santin AD", "date": "2009-06-19", "evidence": [], "reference": [ { "id": "19536090", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/19536090" } ] } ], "biomarker_canonical_id": "AN6295", "score": 2.2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 1 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "c": "condition", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6294-2", "biomarker_component": [ { "biomarker": "increased SAA1 level", "assessed_biomarker_entity": { "recommended_name": "Serum amyloid A protein", "synonyms": [ { "synonym": "SAA" } ] }, "assessed_biomarker_entity_id": "UPKB:P0DJI8", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "32277967", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32277967", "evidence_list": [ { "evidence": "Based on the study results, SAA alone or combined with L(SAA/L) could be used as a significant marker to indicate and track inflammation conditions in COVID-19 infected patients. Monitoring dynamic changes of SAA, combined with CT imaging could be a valuable strategy in the diagnosis and treatment of COVID-19. SAA and L are sensitive indicators in evaluating the severity and prognosis of COVID-19." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32475810", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32475810", "evidence_list": [ { "evidence": "The abnormal increase in serum amyloid protein (SAA) may be used as an auxiliary index for diagnosis and treatment. CRP changes before other blood parameters and thus may be an effective evaluation index for patients with COVID-19 infection. [DOI:10.1101/2020.03.10.20033613] C-reactive protein, serum amyloid A, interleukin-6, lactate dehydrogenase, neutrophil-to-lymphocyte ratio, D-dimer, cardiac troponin, and renal biomarkers showed significantly higher levels in patients with severe complications of COVID-19 infection compared to their non-severe counterparts." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "33735714", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/33735714", "evidence_list": [ { "evidence": "The serum SAA levels were found to be significantly correlated with impending course of the COVID-19, and may serve as a useful biomarker to monitor the complicated clinical course of the disease." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "monitoring" } ], "condition": { "id": "DOID:0080600", "recommended_name": { "id": "DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, "synonyms": [ { "id": "DOID:0080600", "name": "SARS-CoV-2 infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan coronavirus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "COVID19", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan seafood market pneumonia virus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019-nCoV infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019 Novel Coronavirus (2019-nCoV)", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" } ] }, "evidence_source": [ { "id": "32277967", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32277967", "evidence_list": [ { "evidence": "Based on the study results, SAA alone or combined with L(SAA/L) could be used as a significant marker to indicate and track inflammation conditions in COVID-19 infected patients. Monitoring dynamic changes of SAA, combined with CT imaging could be a valuable strategy in the diagnosis and treatment of COVID-19. SAA and L are sensitive indicators in evaluating the severity and prognosis of COVID-19." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32475810", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32475810", "evidence_list": [ { "evidence": "The abnormal increase in serum amyloid protein (SAA) may be used as an auxiliary index for diagnosis and treatment. CRP changes before other blood parameters and thus may be an effective evaluation index for patients with COVID-19 infection. [DOI:10.1101/2020.03.10.20033613] C-reactive protein, serum amyloid A, interleukin-6, lactate dehydrogenase, neutrophil-to-lymphocyte ratio, D-dimer, cardiac troponin, and renal biomarkers showed significantly higher levels in patients with severe complications of COVID-19 infection compared to their non-severe counterparts." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "33735714", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/33735714", "evidence_list": [ { "evidence": "The serum SAA levels were found to be significantly correlated with impending course of the COVID-19, and may serve as a useful biomarker to monitor the complicated clinical course of the disease." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Serum Amyloid A is a biomarker of severe Coronavirus Disease and poor prognosis.", "journal": "The Journal of infection", "authors": "Li H, Xiang X, Ren H, Xu L, Zhao L, Chen X, Long H, Wang Q, Wu Q", "date": "2020-04-12", "evidence": [], "reference": [ { "id": "32277967", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32277967" } ] }, { "title": "The role of biomarkers in diagnosis of COVID-19 - A systematic review.", "journal": "Life sciences", "authors": "Kermali M, Khalsa RK, Pillai K, Ismail Z, Harky A", "date": "2020-06-02", "evidence": [], "reference": [ { "id": "32475810", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32475810" } ] }, { "title": "Serum Amyloid A Protein as a useful biomarker to predict COVID-19 patients severity and prognosis.", "journal": "International immunopharmacology", "authors": "Pieri M, Ciotti M, Nuccetelli M, Perrone MA, Caliò MT, Lia MS, Minieri M, Bernardini S", "date": "2021-03-19", "evidence": [], "reference": [ { "id": "33735714", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/33735714" } ] } ], "biomarker_canonical_id": "AN6294", "score": 1.4, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 2 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6294-3", "biomarker_component": [ { "biomarker": "increased SAA1 level", "assessed_biomarker_entity": { "recommended_name": "Serum amyloid A protein", "synonyms": [ { "synonym": "SAA" } ] }, "assessed_biomarker_entity_id": "UPKB:P0DJI8", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "19470939", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/19470939", "evidence_list": [ { "evidence": "Elevated SAA and CRP were associated with reduced overall survival, regardless of adjustment for age, tumor stage, race, and body mass index (SAA P trend < .0001; CRP P trend = .002). Higher concentrations of SAA were associated with decreased overall survival (P trend < .0001 in all models; lnSAA, P < .01 in all models). Systemic C-reactive protein (CRP) and serum amyloid A (SAA) are measures of low-grade chronic inflammation and potential predictors of cancer survival" } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "name": "breast cancer", "description": "A thoracic cancer that originates in the mammary gland.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, "synonyms": [ { "id": "DOID:1612", "name": "malignant tumor of the breast", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "breast tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "mammary cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "primary breast cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "mammary tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "malignant neoplasm of breast", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" } ] }, "evidence_source": [ { "id": "19470939", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/19470939", "evidence_list": [ { "evidence": "Elevated SAA and CRP were associated with reduced overall survival, regardless of adjustment for age, tumor stage, race, and body mass index (SAA P trend < .0001; CRP P trend = .002). Higher concentrations of SAA were associated with decreased overall survival (P trend < .0001 in all models; lnSAA, P < .01 in all models). Systemic C-reactive protein (CRP) and serum amyloid A (SAA) are measures of low-grade chronic inflammation and potential predictors of cancer survival" } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Elevated biomarkers of inflammation are associated with reduced survival among breast cancer patients.", "journal": "Journal of clinical oncology : official journal of the American Society of Clinical Oncology", "authors": "Pierce BL, Ballard-Barbash R, Bernstein L, Baumgartner RN, Neuhouser ML, Wener MH, Baumgartner KB, Gilliland FD, Sorensen BE, McTiernan A, Ulrich CM", "date": "2009-05-28", "evidence": [], "reference": [ { "id": "19470939", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/19470939" } ] } ], "biomarker_canonical_id": "AN6294", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "f": "frequency", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6296-1", "biomarker_component": [ { "biomarker": "increased CXCL10 level", "assessed_biomarker_entity": { "recommended_name": "IFN-gamma-inducible protein 10", "synonyms": [ { "synonym": "10 kDa interferon gamma-induced protein" }, { "synonym": "Gamma-IP10" }, { "synonym": "IP-10" }, { "synonym": "Small-inducible cytokine B10" } ] }, "assessed_biomarker_entity_id": "UPKB:P02778", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "32360286", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32360286", "evidence_list": [ { "evidence": "IFN-gamma-induced protein 10 and monocyte chemotactic protein-3 were excellent predictors for the progression of COVID-19." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "31986264", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31986264", "evidence_list": [ { "evidence": "We noted that patients infected with 2019-nCoV also had high amounts of IL1B, IFN gamma, IP10, and MCP1, probably leading to activated T-helper-1 (Th1) cell responses. Moreover, patients requiring ICU admission had higher concentrations of GCSF, IP10, MCP1, MIP1A, and TNF alpha than did those not requiring ICU admission, suggesting that the cytokine storm was associated with disease severity." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32360286", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32360286", "evidence_list": [ { "evidence": "IP-10 and MCP-3 were highly associated with disease severity and could be used as excellent predictors of COVID-19 progression." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "monitoring" } ], "condition": { "id": "DOID:0080600", "recommended_name": { "id": "DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, "synonyms": [ { "id": "DOID:0080600", "name": "SARS-CoV-2 infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan coronavirus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "COVID19", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan seafood market pneumonia virus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019-nCoV infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019 Novel Coronavirus (2019-nCoV)", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" } ] }, "evidence_source": [ { "id": "31986264", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31986264", "evidence_list": [ { "evidence": "We noted that patients infected with 2019-nCoV also had high amounts of IL1B, IFN gamma, IP10, and MCP1, probably leading to activated T-helper-1 (Th1) cell responses. Moreover, patients requiring ICU admission had higher concentrations of GCSF, IP10, MCP1, MIP1A, and TNF alpha than did those not requiring ICU admission, suggesting that the cytokine storm was associated with disease severity." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32360286", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32360286", "evidence_list": [ { "evidence": "IP-10 and MCP-3 were highly associated with disease severity and could be used as excellent predictors of COVID-19 progression." }, { "evidence": "IFN-gamma-induced protein 10 and monocyte chemotactic protein-3 were excellent predictors for the progression of COVID-19." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Plasma IP-10 and MCP-3 levels are highly associated with disease severity and predict the progression of COVID-19.", "journal": "The Journal of allergy and clinical immunology", "authors": "Yang Y, Shen C, Li J, Yuan J, Wei J, Huang F, Wang F, Li G, Li Y, Xing L, Peng L, Yang M, Cao M, Zheng H, Wu W, Zou R, Li D, Xu Z, Wang H, Zhang M, Zhang Z, Gao GF, Jiang C, Liu L, Liu Y", "date": "2020-05-04", "evidence": [], "reference": [ { "id": "32360286", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32360286" } ] }, { "title": "Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China.", "journal": "Lancet (London, England)", "authors": "Huang C, Wang Y, Li X, Ren L, Zhao J, Hu Y, Zhang L, Fan G, Xu J, Gu X, Cheng Z, Yu T, Xia J, Wei Y, Wu W, Xie X, Yin W, Li H, Liu M, Xiao Y, Gao H, Guo L, Xie J, Wang G, Jiang R, Gao Z, Jin Q, Wang J, Cao B", "date": "2020-01-28", "evidence": [], "reference": [ { "id": "31986264", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31986264" } ] } ], "biomarker_canonical_id": "AN6296", "score": 1.2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 1 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "c": "condition", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6297-1", "biomarker_component": [ { "biomarker": "increased CCL7 level", "assessed_biomarker_entity": { "recommended_name": "Monocyte chemotactic protein-3", "synonyms": [ { "synonym": "Monocyte chemoattractant protein 3" }, { "synonym": "Monocyte chemotactic protein 3" }, { "synonym": "MCP-3" }, { "synonym": "NC28" }, { "synonym": "Small-inducible cytokine A7" } ] }, "assessed_biomarker_entity_id": "UPKB:P80098", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "31986264", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31986264", "evidence_list": [ { "evidence": "We noted that patients infected with 2019-nCoV also had high amounts of IL1B, IFN gamma, IP10, and MCP1, probably leading to activated T-helper-1 (Th1) cell responses. 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Moreover, patients requiring ICU admission had higher concentrations of GCSF, IP10, MCP1, MIP1A, and TNF alpha than did those not requiring ICU admission, suggesting that the cytokine storm was associated with disease severity." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China.", "journal": "Lancet (London, England)", "authors": "Huang C, Wang Y, Li X, Ren L, Zhao J, Hu Y, Zhang L, Fan G, Xu J, Gu X, Cheng Z, Yu T, Xia J, Wei Y, Wu W, Xie X, Yin W, Li H, Liu M, Xiao Y, Gao H, Guo L, Xie J, Wang G, Jiang R, Gao Z, Jin Q, Wang J, Cao B", "date": "2020-01-28", "evidence": [], "reference": [ { "id": "31986264", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31986264" } ] }, { "title": "Plasma IP-10 and MCP-3 levels are highly associated with disease severity and predict the progression of COVID-19.", "journal": "The Journal of allergy and clinical immunology", "authors": "Yang Y, Shen C, Li J, Yuan J, Wei J, Huang F, Wang F, Li G, Li Y, Xing L, Peng L, Yang M, Cao M, Zheng H, Wu W, Zou R, Li D, Xu Z, Wang H, Zhang M, Zhang Z, Gao GF, Jiang C, Liu L, Liu Y", "date": "2020-05-04", "evidence": [], "reference": [ { "id": "32360286", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32360286" } ] } ], "biomarker_canonical_id": "AN6297", "score": 1.2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 1 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "f": "frequency", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6298-1", "biomarker_component": [ { "biomarker": "increased CCL7 level", "assessed_biomarker_entity": { "recommended_name": "Monocyte chemotactic protein-3", "synonyms": [ { "synonym": "FIC" }, { "synonym": "MARC" }, { "synonym": "MCP-3" }, { "synonym": "MCP3" }, { "synonym": "NC28" }, { "synonym": "SCYA6" }, { "synonym": "SCYA7" } ] }, "assessed_biomarker_entity_id": "NCBI: 6354", "assessed_entity_type": "gene", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "12439927", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/12439927", "evidence_list": [ { "evidence": "We detected MCP-3 mRNA expression in MCP-3 gene transfected CMT93 cells. In contrast, the wild type CMT93 cells and the mock transfected CMT93 cells did not express MCP-3. In the tumor tissue derived from CMT93/MCP-3, infiltrating immune cells increased. In addition, no tumor metastasis was found in all mice inoculated with CMT93/ MCP-3 tumor cells. But all mice had tumor metastasis in CMT93 controls. In our study, we found that after the transfecting of CMT93 colorectal cancer cell with MCP-3 gene, tumor growth was retarded and tumor metastasis was inhibited completely by promoting immune cells infiltration in tumor tissue." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_9256" }, "synonyms": [] }, "evidence_source": [ { "id": "12439927", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/12439927", "evidence_list": [ { "evidence": "We detected MCP-3 mRNA expression in MCP-3 gene transfected CMT93 cells. In contrast, the wild type CMT93 cells and the mock transfected CMT93 cells did not express MCP-3. In the tumor tissue derived from CMT93/MCP-3, infiltrating immune cells increased. In addition, no tumor metastasis was found in all mice inoculated with CMT93/ MCP-3 tumor cells. But all mice had tumor metastasis in CMT93 controls. In our study, we found that after the transfecting of CMT93 colorectal cancer cell with MCP-3 gene, tumor growth was retarded and tumor metastasis was inhibited completely by promoting immune cells infiltration in tumor tissue." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Transfection of colorectal cancer cells with chemokine MCP-3 (monocyte chemotactic protein-3) gene retards tumor growth and inhibits tumor metastasis.", "journal": "World journal of gastroenterology", "authors": "Hu JY, Li GC, Wang WM, Zhu JG, Li YF, Zhou GH, Sun QB", "date": "2002-11-20", "evidence": [], "reference": [ { "id": "12439927", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/12439927" } ] } ], "biomarker_canonical_id": "AN6298", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "f": "frequency", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6299-1", "biomarker_component": [ { "biomarker": "increased GRAN count", "assessed_biomarker_entity": { "recommended_name": "Granulocyte", "synonyms": [ { "synonym": "granular leucocyte" }, { "synonym": "granular leukocyte" }, { "synonym": "polymorphonuclear leukocyte" } ] }, "assessed_biomarker_entity_id": "CO:CL_0000094", "assessed_entity_type": "cell", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "30394-1" } ], "evidence_source": [ { "id": "32281668", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32281668", "evidence_list": [ { "evidence": "Patients with flu had higher WBC, granulocyte and granulocyte/lymphocyte ratio, compared with COVID-19 patients." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:0080600", "recommended_name": { "id": "DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, "synonyms": [ { "id": "DOID:0080600", "name": "SARS-CoV-2 infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan coronavirus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "COVID19", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan seafood market pneumonia virus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019-nCoV infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019 Novel Coronavirus (2019-nCoV)", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" } ] }, "evidence_source": [ { "id": "32281668", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32281668", "evidence_list": [ { "evidence": "Patients with flu had higher WBC, granulocyte and granulocyte/lymphocyte ratio, compared with COVID-19 patients." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "C-reactive protein correlates with computed tomographic findings and predicts severe COVID-19 early.", "journal": "Journal of medical virology", "authors": "Tan C, Huang Y, Shi F, Tan K, Ma Q, Chen Y, Jiang X, Li X", "date": "2020-04-14", "evidence": [], "reference": [ { "id": "32281668", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32281668" } ] } ], "biomarker_canonical_id": "AN6299", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "f": "frequency", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6299-2", "biomarker_component": [ { "biomarker": "increased GRAN count", "assessed_biomarker_entity": { "recommended_name": "Granulocyte", "synonyms": [ { "synonym": "granular leucocyte" }, { "synonym": "granular leukocyte" }, { "synonym": "polymorphonuclear leukocyte" } ] }, "assessed_biomarker_entity_id": "CO:CL_0000094", "assessed_entity_type": "cell", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "30394-1" } ], "evidence_source": [ { "id": "11406548", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/11406548", "evidence_list": [ { "evidence": "The chronic presence of the tumor and thus chronic activation of granulocytes with the accompanying production of H2O2 results, ironically, in the suppression of the adaptive immune functions. Here we show specifically that the release of reactive oxygen species during the oxidative burst of granulocytes, i.e., H2O2, is the major contributor to a systemic T-cell dysfunction. This is supported by the observation that cancer patients showed signs of extensive granulocyte activation with massive elevation of plasma levels of 8-isoprostane, a product of lipid oxidation and a marker for oxidative stress, that exceeded measurements found in other diseases with documented oxidative stress." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "name": "advanced cancer", "description": "A thoracic cancer that originates in the mammary gland.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, "synonyms": [ { "id": "DOID:1612", "name": "malignant tumor of the breast", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "breast tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "mammary cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "primary breast cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "mammary tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "malignant neoplasm of breast", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" } ] }, "evidence_source": [ { "id": "11406548", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/11406548", "evidence_list": [ { "evidence": "The chronic presence of the tumor and thus chronic activation of granulocytes with the accompanying production of H2O2 results, ironically, in the suppression of the adaptive immune functions. Here we show specifically that the release of reactive oxygen species during the oxidative burst of granulocytes, i.e., H2O2, is the major contributor to a systemic T-cell dysfunction. This is supported by the observation that cancer patients showed signs of extensive granulocyte activation with massive elevation of plasma levels of 8-isoprostane, a product of lipid oxidation and a marker for oxidative stress, that exceeded measurements found in other diseases with documented oxidative stress." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Activated granulocytes and granulocyte-derived hydrogen peroxide are the underlying mechanism of suppression of t-cell function in advanced cancer patients.", "journal": "Cancer research", "authors": "Schmielau J, Finn OJ", "date": "2001-06-19", "evidence": [], "reference": [ { "id": "11406548", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/11406548" } ] } ], "biomarker_canonical_id": "AN6299", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6745-1", "biomarker_component": [ { "biomarker": "Increased D-dimer level", "assessed_biomarker_entity": { "recommended_name": "D-dimer", "synonyms": [] }, "assessed_biomarker_entity_id": "PRO:PR_000050369", "assessed_entity_type": "protein complex", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "71427-9" } ], "evidence_source": [ { "id": "32677844", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32677844", "evidence_list": [ { "evidence": "Elevated levels of IL-6, D-dimer, CRP, LDH, and ferritin all had an independent increased risk for the clinical outcomes assessed (ICU admission, invasive ventilatory support and death), which were statistically significant." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32475810", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32475810", "evidence_list": [ { "evidence": "C-reactive protein, serum amyloid A, interleukin-6, lactate dehydrogenase, neutrophil-to-lymphocyte ratio, D-dimer, cardiac troponin, and renal biomarkers showed significantly higher levels in patients with severe complications of COVID-19 infection compared to their non-severe counterparts." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32442528", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32442528", "evidence_list": [ { "evidence": "Findings in this study include determining independent associations between biomarkers for inflammation (interleukin-6) and thrombosis (D-dimer) and mortality." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32220650", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32220650", "evidence_list": [ { "evidence": "Besides radiographic presentations, variables that were associated significantly with severity of COVID-19 were decreased lymphocytes, elevated body temperature, and high levels of procalcitonin, D-dimer, and creatine kinase MB." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32171076", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32171076", "evidence_list": [ { "evidence": "Age, comorbidities, lymphocytopenia and elevated alanine aminotransferase, d-dimer, creatine kinase, high-sensitivity cardiac troponin I, prothrombin time, and disease severity were reported to be associated with intensive care unit admission." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32306492", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32306492", "evidence_list": [ { "evidence": "Patients with D-dimer levels >/=2.0 ¬µg/mL had a higher incidence of mortality when comparing with those who with D-dimer levels <2.0 ¬µg/mL (12/67 vs 1/267, P < .001; hazard ratio, 51.5; 95% confidence interval, 12.9-206.7)." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32665858", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32665858", "evidence_list": [ { "evidence": "D-dimer is commonly elevated in patients with COVID-19. D-dimer levels correlate with disease severity and is a reliable prognostic marker for in-hospital mortality in patients admitted for COVID-19." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32620118", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32620118", "evidence_list": [ { "evidence": "The rising trend in D-Dimer and NLR, or the test results higher than the critical values may indicate a risk of death for participants with COVID-19." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32475810", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32475810", "evidence_list": [ { "evidence": "This, along with the previous study, suggests that D-dimer levels can be used as a prognostic marker and help clinicians monitor those who are likely to deteriorate earlier." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32172226", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32172226", "evidence_list": [ { "evidence": "D-dimer (10.36 vs. 0.26 ng/L; p<0.001) were higher in patients with SARS-CoV-2 than those in controls." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32367765", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32367765", "evidence_list": [ { "evidence": "The most important finding was that FAR and PLT count were independent risk factors to predict the development of severe illness in COVID-19. Patients with FAR<0.0883 and PLT count>135*10^9/L were unlikely to develop into severe disease." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32073213", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32073213", "evidence_list": [ { "evidence": "Non-survivors revealed significantly higher D-dimer and fibrin degradation product (FDP) levels, longer prothrombin time and activated partial thromboplastin time." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32181911", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32181911", "evidence_list": [ { "evidence": "IL-6 and D-dimer were closely related to the occurrence of severe COVID-19 in the adult patients, and their combined detection had the highest specificity and sensitivity for early prediction of the severity of COVID-19 patients, which has important clinical value." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32430456", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32430456", "evidence_list": [ { "evidence": "The mean of glycemia during hospitalization was 10.65 ¬± 0.84 mmol/L in the no insulin infusion group and 7.69 ¬± 1.85 mmol/L in the insulin infusion group. At baseline, IL-6 and D-dimer levels were significantly higher in the hyperglycemic group than in the normoglycemic group (P < 0.001). Even though all patients were on standard treatment for COVID-19 infection, IL-6 and D-dimer levels persisted higher in patients with hyperglycemia during hospitalization." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32623030", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32623030", "evidence_list": [ { "evidence": "In COVID-19 patients with diabetes, poorly-controlled blood glucose (>11 mmol/L) may be associated with poor outcomes. Admission hyperglycemia, elevated d-dimer and high HRCT score are potential risk factors for adverse outcomes and death." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32357994", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32357994", "evidence_list": [ { "evidence": "Post-COVID-19 infection, lower hemoglobin levels, higher total white blood cell (WBC) counts, and higher absolute neutrophil counts were associated with increased mortality. Analysis of other serologic biomarkers demonstrated that elevated D-dimer, lactate, and lactate dehydrogenase (LDH) in patients were significantly correlated with dying." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32369209", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32369209", "evidence_list": [ { "evidence": "Low lymphocytes, increased IL-6, CRP, PCT, D dimer, and LDH indicates that the infected patients were in inflammatory state, which may be closely related to the inflammatory storm. The increase of the cancer biomarkers in patients with COVID-19, especially in severe and critical patients, suggests that inflammation is closely related to the development of COVID-19." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32369209", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32369209", "evidence_list": [ { "evidence": "Our results showed that the laboratory tests of cancer patients had the following characteristics: low lymphocytes, increased IL-6, CRP, PCT, D dimer, and LDH. The increase of these inflammatory indexes indicates that the infected patients were in inflammatory state, which may be closely related to the inflammatory storm." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32503382", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32503382", "evidence_list": [ { "evidence": "Erythrocyte sedimentation rate (ESR) (R=0.55, p < .01) was positively associated with CT severity scores. To sum up, we can conclude from the analysis of published studies that hematological (lymphocyte count, neutrophil count, and NLR), inflammatory (CRP, ESR, IL-6), and especially biochemical (D-dimer, Troponins, CK) parameters correlate with severe prognosis or exitus in COVID-19 patients and can therefore be used as predictive biomarkers." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "monitoring" } ], "condition": { "id": "DOID:0080600", "recommended_name": { "id": "DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, "synonyms": [ { "id": "DOID:0080600", "name": "SARS-CoV-2 infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan coronavirus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "COVID19", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan seafood market pneumonia virus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019-nCoV infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019 Novel Coronavirus (2019-nCoV)", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" } ] }, "evidence_source": [ { "id": "32677844", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32677844", "evidence_list": [ { "evidence": "Elevated levels of IL-6, D-dimer, CRP, LDH, and ferritin all had an independent increased risk for the clinical outcomes assessed (ICU admission, invasive ventilatory support and death), which were statistically significant." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32442528", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32442528", "evidence_list": [ { "evidence": "Findings in this study include determining independent associations between biomarkers for inflammation (interleukin-6) and thrombosis (D-dimer) and mortality." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32220650", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32220650", "evidence_list": [ { "evidence": "Besides radiographic presentations, variables that were associated significantly with severity of COVID-19 were decreased lymphocytes, elevated body temperature, and high levels of procalcitonin, D-dimer, and creatine kinase MB." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32171076", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32171076", "evidence_list": [ { "evidence": "Age, comorbidities, lymphocytopenia and elevated alanine aminotransferase, d-dimer, creatine kinase, high-sensitivity cardiac troponin I, prothrombin time, and disease severity were reported to be associated with intensive care unit admission." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32306492", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32306492", "evidence_list": [ { "evidence": "Patients with D-dimer levels >/=2.0 ¬µg/mL had a higher incidence of mortality when comparing with those who with D-dimer levels <2.0 ¬µg/mL (12/67 vs 1/267, P < .001; hazard ratio, 51.5; 95% confidence interval, 12.9-206.7)." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32665858", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32665858", "evidence_list": [ { "evidence": "D-dimer is commonly elevated in patients with COVID-19. D-dimer levels correlate with disease severity and is a reliable prognostic marker for in-hospital mortality in patients admitted for COVID-19." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32620118", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32620118", "evidence_list": [ { "evidence": "The rising trend in D-Dimer and NLR, or the test results higher than the critical values may indicate a risk of death for participants with COVID-19." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32172226", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32172226", "evidence_list": [ { "evidence": "D-dimer (10.36 vs. 0.26 ng/L; p<0.001) were higher in patients with SARS-CoV-2 than those in controls." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32367765", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32367765", "evidence_list": [ { "evidence": "The most important finding was that FAR and PLT count were independent risk factors to predict the development of severe illness in COVID-19. Patients with FAR<0.0883 and PLT count>135*10^9/L were unlikely to develop into severe disease." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32073213", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32073213", "evidence_list": [ { "evidence": "Non-survivors revealed significantly higher D-dimer and fibrin degradation product (FDP) levels, longer prothrombin time and activated partial thromboplastin time." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32181911", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32181911", "evidence_list": [ { "evidence": "IL-6 and D-dimer were closely related to the occurrence of severe COVID-19 in the adult patients, and their combined detection had the highest specificity and sensitivity for early prediction of the severity of COVID-19 patients, which has important clinical value." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32430456", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32430456", "evidence_list": [ { "evidence": "The mean of glycemia during hospitalization was 10.65 ¬± 0.84 mmol/L in the no insulin infusion group and 7.69 ¬± 1.85 mmol/L in the insulin infusion group. At baseline, IL-6 and D-dimer levels were significantly higher in the hyperglycemic group than in the normoglycemic group (P < 0.001). Even though all patients were on standard treatment for COVID-19 infection, IL-6 and D-dimer levels persisted higher in patients with hyperglycemia during hospitalization." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32623030", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32623030", "evidence_list": [ { "evidence": "In COVID-19 patients with diabetes, poorly-controlled blood glucose (>11 mmol/L) may be associated with poor outcomes. Admission hyperglycemia, elevated d-dimer and high HRCT score are potential risk factors for adverse outcomes and death." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32357994", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32357994", "evidence_list": [ { "evidence": "Post-COVID-19 infection, lower hemoglobin levels, higher total white blood cell (WBC) counts, and higher absolute neutrophil counts were associated with increased mortality. Analysis of other serologic biomarkers demonstrated that elevated D-dimer, lactate, and lactate dehydrogenase (LDH) in patients were significantly correlated with dying." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32369209", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32369209", "evidence_list": [ { "evidence": "Low lymphocytes, increased IL-6, CRP, PCT, D dimer, and LDH indicates that the infected patients were in inflammatory state, which may be closely related to the inflammatory storm. The increase of the cancer biomarkers in patients with COVID-19, especially in severe and critical patients, suggests that inflammation is closely related to the development of COVID-19." }, { "evidence": "Our results showed that the laboratory tests of cancer patients had the following characteristics: low lymphocytes, increased IL-6, CRP, PCT, D dimer, and LDH. The increase of these inflammatory indexes indicates that the infected patients were in inflammatory state, which may be closely related to the inflammatory storm." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32503382", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32503382", "evidence_list": [ { "evidence": "Erythrocyte sedimentation rate (ESR) (R=0.55, p < .01) was positively associated with CT severity scores. To sum up, we can conclude from the analysis of published studies that hematological (lymphocyte count, neutrophil count, and NLR), inflammatory (CRP, ESR, IL-6), and especially biochemical (D-dimer, Troponins, CK) parameters correlate with severe prognosis or exitus in COVID-19 patients and can therefore be used as predictive biomarkers." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32475810", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32475810", "evidence_list": [ { "evidence": "C-reactive protein, serum amyloid A, interleukin-6, lactate dehydrogenase, neutrophil-to-lymphocyte ratio, D-dimer, cardiac troponin, and renal biomarkers showed significantly higher levels in patients with severe complications of COVID-19 infection compared to their non-severe counterparts." }, { "evidence": "This, along with the previous study, suggests that D-dimer levels can be used as a prognostic marker and help clinicians monitor those who are likely to deteriorate earlier." } ], "tags": [ { "tag": "condition" }, { "tag": "best_biomarker_role" } ] }, { "id": "32589600", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32589600", "evidence_list": [ { "evidence": "Many biomarkers have been associated with poor outcomes and represent a candidate for risk stratification models for predicting severe COVID-19 in order to guide clinical care. Among all, lymphopenia, thrombocytopenia, leucocytosis, CRP, PCT, LDH, AST, ALT, D-dimer, cTn represent the most predictive parameters of severe COVID-19" } ], "tags": [ { "tag": "condition" }, { "tag": "best_biomarker_role" } ] } ], "citation": [ { "title": "The association between biomarkers and clinical outcomes in novel coronavirus pneumonia in a US cohort.", "journal": "Biomarkers in medicine", "authors": "Ayanian S, Reyes J, Lynn L, Teufel K", "date": "2020-07-18", "evidence": [], "reference": [ { "id": "32677844", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32677844" } ] }, { "title": "The role of biomarkers in diagnosis of COVID-19 - A systematic review.", "journal": "Life sciences", "authors": "Kermali M, Khalsa RK, Pillai K, Ismail Z, Harky A", "date": "2020-06-02", "evidence": [], "reference": [ { "id": "32475810", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32475810" } ] }, { "title": "Epidemiology, clinical course, and outcomes of critically ill adults with COVID-19 in New York City: a prospective cohort study.", "journal": "Lancet (London, England)", "authors": "Cummings MJ, Baldwin MR, Abrams D, Jacobson SD, Meyer BJ, Balough EM, Aaron JG, Claassen J, Rabbani LE, Hastie J, Hochman BR, Salazar-Schicchi J, Yip NH, Brodie D, O'Donnell MR", "date": "2020-05-23", "evidence": [], "reference": [ { "id": "32442528", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32442528" } ] }, { "title": "Clinical and epidemiological features of 36 children with coronavirus disease 2019 (COVID-19) in Zhejiang, China: an observational cohort study.", "journal": "The Lancet. Infectious diseases", "authors": "Qiu H, Wu J, Hong L, Luo Y, Song Q, Chen D", "date": "2020-03-30", "evidence": [], "reference": [ { "id": "32220650", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32220650" } ] }, { "title": "Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: a retrospective cohort study.", "journal": "Lancet (London, England)", "authors": "Zhou F, Yu T, Du R, Fan G, Liu Y, Liu Z, Xiang J, Wang Y, Song B, Gu X, Guan L, Wei Y, Li H, Wu X, Xu J, Tu S, Zhang Y, Chen H, Cao B", "date": "2020-03-15", "evidence": [], "reference": [ { "id": "32171076", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32171076" } ] }, { "title": "D-dimer levels on admission to predict in-hospital mortality in patients with Covid-19.", "journal": "Journal of thrombosis and haemostasis : JTH", "authors": "Zhang L, Yan X, Fan Q, Liu H, Liu X, Liu Z, Zhang Z", "date": "2020-04-20", "evidence": [], "reference": [ { "id": "32306492", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32306492" } ] }, { "title": "D-dimer as a biomarker for disease severity and mortality in COVID-19 patients: a case control study.", "journal": "Journal of intensive care", "authors": "Yao Y, Cao J, Wang Q, Shi Q, Liu K, Luo Z, Chen X, Chen S, Yu K, Huang Z, Hu B", "date": "2020-07-16", "evidence": [], "reference": [ { "id": "32665858", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32665858" } ] }, { "title": "Dynamic changes of D-dimer and neutrophil-lymphocyte count ratio as prognostic biomarkers in COVID-19.", "journal": "Respiratory research", "authors": "Ye W, Chen G, Li X, Lan X, Ji C, Hou M, Zhang D, Zeng G, Wang Y, Xu C, Lu W, Cui R, Cai Y, Huang H, Yang L", "date": "2020-07-06", "evidence": [], "reference": [ { "id": "32620118", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32620118" } ] }, { "title": "Prominent changes in blood coagulation of patients with SARS-CoV-2 infection.", "journal": "Clinical chemistry and laboratory medicine", "authors": "Han H, Yang L, Liu R, Liu F, Wu KL, Li J, Liu XH, Zhu CL", "date": "2020-03-17", "evidence": [], "reference": [ { "id": "32172226", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32172226" } ] }, { "title": "Prediction of severe illness due to COVID-19 based on an analysis of initial Fibrinogen to Albumin Ratio and Platelet count.", "journal": "Platelets", "authors": "Bi X, Su Z, Yan H, Du J, Wang J, Chen L, Peng M, Chen S, Shen B, Li J", "date": "2020-05-06", "evidence": [], "reference": [ { "id": "32367765", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32367765" } ] }, { "title": "Abnormal coagulation parameters are associated with poor prognosis in patients with novel coronavirus pneumonia.", "journal": "Journal of thrombosis and haemostasis : JTH", "authors": "Tang N, Li D, Wang X, Sun Z", "date": "2020-02-20", "evidence": [], "reference": [ { "id": "32073213", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32073213" } ] }, { "title": "Diagnostic utility of clinical laboratory data determinations for patients with the severe COVID-19.", "journal": "Journal of medical virology", "authors": "Gao Y, Li T, Han M, Li X, Wu D, Xu Y, Zhu Y, Liu Y, Wang X, Wang L", "date": "2020-03-18", "evidence": [], "reference": [ { "id": "32181911", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32181911" } ] }, { "title": "Outcomes in Patients With Hyperglycemia Affected by COVID-19: Can We Do More on Glycemic Control?", "journal": "Diabetes care", "authors": "Sardu C, D'Onofrio N, Balestrieri ML, Barbieri M, Rizzo MR, Messina V, Maggi P, Coppola N, Paolisso G, Marfella R", "date": "2020-05-21", "evidence": [], "reference": [ { "id": "32430456", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32430456" } ] }, { "title": "Baseline characteristics and risk factors for short-term outcomes in 132 COVID-19 patients with diabetes in Wuhan China: A retrospective study.", "journal": "Diabetes research and clinical practice", "authors": "Li Y, Han X, Alwalid O, Cui Y, Cao Y, Liu J, Gu J, Wang L, Fan Y, Shi H", "date": "2020-07-06", "evidence": [], "reference": [ { "id": "32623030", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32623030" } ] }, { "title": "Case Fatality Rate of Cancer Patients with COVID-19 in a New York Hospital System.", "journal": "Cancer discovery", "authors": "Mehta V, Goel S, Kabarriti R, Cole D, Goldfinger M, Acuna-Villaorduna A, Pradhan K, Thota R, Reissman S, Sparano JA, Gartrell BA, Smith RV, Ohri N, Garg M, Racine AD, Kalnicki S, Perez-Soler R, Halmos B, Verma A", "date": "2020-05-03", "evidence": [], "reference": [ { "id": "32357994", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32357994" } ] }, { "title": "Clinical characteristics and outcomes of cancer patients with COVID-19.", "journal": "Journal of medical virology", "authors": "Yang F, Shi S, Zhu J, Shi J, Dai K, Chen X", "date": "2020-05-06", "evidence": [], "reference": [ { "id": "32369209", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32369209" } ] }, { "title": "Biomarkers associated with COVID-19 disease progression.", "journal": "Critical reviews in clinical laboratory sciences", "authors": "Ponti G, Maccaferri M, Ruini C, Tomasi A, Ozben T", "date": "2020-06-07", "evidence": [], "reference": [ { "id": "32503382", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32503382" } ] }, { "title": "Biochemical biomarkers alterations in Coronavirus Disease 2019 (COVID-19).", "journal": "Diagnosis (Berlin, Germany)", "authors": "Ciaccio M, Agnello L", "date": "2020-06-27", "evidence": [], "reference": [ { "id": "32589600", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32589600" } ] } ], "biomarker_canonical_id": "AN6745", "score": 3.8, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 9 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "f": "frequency", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6301-1", "biomarker_component": [ { "biomarker": "Increased NLR level", "assessed_biomarker_entity": { "recommended_name": "Neutrophil-Lymphocyte Ratio", "synonyms": [] }, "assessed_biomarker_entity_id": "NCIt:C141271", "assessed_entity_type": "cell", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "71427-9" } ], "evidence_source": [ { "id": "32620118", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32620118", "evidence_list": [ { "evidence": "The rising trend in D-Dimer and NLR, or the test results higher than the critical values may indicate a risk of death for participants with COVID-19." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "monitoring" } ], "condition": { "id": "DOID:0080600", "recommended_name": { "id": "DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, "synonyms": [ { "id": "DOID:0080600", "name": "SARS-CoV-2 infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan coronavirus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "COVID19", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan seafood market pneumonia virus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019-nCoV infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019 Novel Coronavirus (2019-nCoV)", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" } ] }, "evidence_source": [ { "id": "32620118", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32620118", "evidence_list": [ { "evidence": "The rising trend in D-Dimer and NLR, or the test results higher than the critical values may indicate a risk of death for participants with COVID-19." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Dynamic changes of D-dimer and neutrophil-lymphocyte count ratio as prognostic biomarkers in COVID-19.", "journal": "Respiratory research", "authors": "Ye W, Chen G, Li X, Lan X, Ji C, Hou M, Zhang D, Zeng G, Wang Y, Xu C, Lu W, Cui R, Cai Y, Huang H, Yang L", "date": "2020-07-06", "evidence": [], "reference": [ { "id": "32620118", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32620118" } ] } ], "biomarker_canonical_id": "AN6301", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6302-1", "biomarker_component": [ { "biomarker": "Elevated FDP level", "assessed_biomarker_entity": { "recommended_name": "Fibrin degradation product", "synonyms": [] }, "assessed_biomarker_entity_id": "NCIt:C82013", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "71427-9" } ], "evidence_source": [ { "id": "32073213", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32073213", "evidence_list": [ { "evidence": "Non-survivors revealed significantly higher D-dimer and fibrin degradation product (FDP) levels, longer prothrombin time and activated partial thromboplastin time." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "monitoring" } ], "condition": { "id": "DOID:0080600", "recommended_name": { "id": "DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, "synonyms": [ { "id": "DOID:0080600", "name": "SARS-CoV-2 infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan coronavirus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "COVID19", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan seafood market pneumonia virus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019-nCoV infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019 Novel Coronavirus (2019-nCoV)", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" } ] }, "evidence_source": [ { "id": "32073213", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32073213", "evidence_list": [ { "evidence": "Non-survivors revealed significantly higher D-dimer and fibrin degradation product (FDP) levels, longer prothrombin time and activated partial thromboplastin time." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Abnormal coagulation parameters are associated with poor prognosis in patients with novel coronavirus pneumonia.", "journal": "Journal of thrombosis and haemostasis : JTH", "authors": "Tang N, Li D, Wang X, Sun Z", "date": "2020-02-20", "evidence": [], "reference": [ { "id": "32073213", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32073213" } ] } ], "biomarker_canonical_id": "AN6302", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "c": "condition", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6745-2", "biomarker_component": [ { "biomarker": "Increased D-dimer level", "assessed_biomarker_entity": { "recommended_name": "D-dimer", "synonyms": [] }, "assessed_biomarker_entity_id": "PRO:PR_000050369", "assessed_entity_type": "protein complex", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "71427-9" } ], "evidence_source": [ { "id": "17454757", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/17454757", "evidence_list": [ { "evidence": "We report changes in D-dimer levels that may indicate diabetes disease progression to macrovascular complications. Using D-dimer in conjunction with other biomarkers to identify stages of disease progression, commencing from pre-diabetes and continuing to development of asymptomatic and clinical cardiovascular disease in diabetes mellitus, is worthy of consideration." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:9351", "recommended_name": { "id": "DOID:9351", "name": "diabetes mellitus", "description": "A glucose metabolism disease that is characterized by chronic hyperglycaemia with disturbances of carbohydrate, fat and protein metabolism resulting from defects in insulin secretion, insulin action, or both.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_9351" }, "synonyms": [ { "id": "DOID:9351", "name": "diabetes", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_9351" } ] }, "evidence_source": [ { "id": "17454757", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/17454757", "evidence_list": [ { "evidence": "We report changes in D-dimer levels that may indicate diabetes disease progression to macrovascular complications. Using D-dimer in conjunction with other biomarkers to identify stages of disease progression, commencing from pre-diabetes and continuing to development of asymptomatic and clinical cardiovascular disease in diabetes mellitus, is worthy of consideration." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "D-dimer identifies stages in the progression of diabetes mellitus from family history of diabetes to cardiovascular complications.", "journal": "Pathology", "authors": "Nwose EU, Richards RS, Jelinek HF, Kerr PG", "date": "2007-04-25", "evidence": [], "reference": [ { "id": "17454757", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/17454757" } ] } ], "biomarker_canonical_id": "AN6745", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6305-1", "biomarker_component": [ { "biomarker": "increased LDH level", "assessed_biomarker_entity": { "recommended_name": "Lactate dehydrogenase", "synonyms": [] }, "assessed_biomarker_entity_id": "PRO:PR_000050367", "assessed_entity_type": "protein complex", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "14804-9" } ], "evidence_source": [ { "id": "32677844", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32677844", "evidence_list": [ { "evidence": "Elevated levels of IL-6, D-dimer, CRP, LDH, and ferritin all had an independent increased risk for the clinical outcomes assessed (ICU admission, invasive ventilatory support and death), which were statistically significant." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32475810", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32475810", "evidence_list": [ { "evidence": "Serum urea, CREA, CysC, DBIL, CHE and LDH could be used to distinguish severe COVID-19 cases from mild COVID-19 cases. [DOI:10.1101/2020.03.19.20034447] Biomarkers that predict the mortality of individual patients more than 10 days in advance with more than 90% accuracy: lactic dehydrogenase (LDH), lymphocyte and high-sensitivity C-reactive protein (hs-CRP). [DOI:10.1038/s42256-020-0180-7] Since high levels of LDH continued in the ICU patients number of days post-admission, LDH may be a predictive biomarker of severe disease. There is increasing confidence in using LDH as a biomarker to measure severity of COVID-19 infection." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32296824", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32296824", "evidence_list": [ { "evidence": "We found that old age, and higher serum lactate dehydrogenase, C-reactive protein, the coefficient of variation of red blood cell distribution width, blood urea nitrogen, direct bilirubin, lower albumin, are associated with severe COVID-19." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32161968", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32161968", "evidence_list": [ { "evidence": "LDH and alpha-HBDH may be considerable markers for evaluation of NCOVID-19." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32475810", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32475810", "evidence_list": [ { "evidence": "C-reactive protein, serum amyloid A, interleukin-6, lactate dehydrogenase, neutrophil-to-lymphocyte ratio, D-dimer, cardiac troponin, and renal biomarkers showed significantly higher levels in patients with severe complications of COVID-19 infection compared to their non-severe counterparts." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32311826", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32311826", "evidence_list": [ { "evidence": "As would be anticipated, elevation is LDH is common in COVID-19 patients in the ICU setting and indicates a poor outcome." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32048163", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32048163", "evidence_list": [ { "evidence": "Biomarkers that predict the mortality of individual patients more than 10 days in advance with more than 90% accuracy: lactic dehydrogenase (LDH), lymphocyte and high-sensitivity C-reactive protein (hs-CRP). [DOI:10.1038/s42256-020-0180-7] The combinations of the hypoalbuminemia, lymphopenia, and high concentrations of CRP and LDH in 2019-nCoV infected patients upon hospital admission may predict more severe acute lung injury." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32738466", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32738466", "evidence_list": [ { "evidence": "Elevated LDH levels were associated with a ~6-fold increase in odds of developing severe disease and a ~16-fold increase in odds of mortality in patients with COVID-19." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32369209", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32369209", "evidence_list": [ { "evidence": "Our results showed that the laboratory tests of cancer patients had the following characteristics: low lymphocytes, increased IL-6, CRP, PCT, D dimer, and LDH. The increase of these inflammatory indexes indicates that the infected patients were in inflammatory state, which may be closely related to the inflammatory storm." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32357994", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32357994", "evidence_list": [ { "evidence": "Post-COVID-19 infection, lower hemoglobin levels, higher total white blood cell (WBC) counts, and higher absolute neutrophil counts were associated with increased mortality. Analysis of other serologic biomarkers demonstrated that elevated D-dimer, lactate, and lactate dehydrogenase (LDH) in patients were significantly correlated with dying." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32259132", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32259132", "evidence_list": [ { "evidence": "Our findings suggest that level of LDH, CRP, ALT and NEU can be used to predict the result of COVID-19 test." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32369209", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32369209", "evidence_list": [ { "evidence": "Low lymphocytes, increased IL-6, CRP, PCT, D dimer, and LDH indicates that the infected patients were in inflammatory state, which may be closely related to the inflammatory storm. The increase of the cancer biomarkers in patients with COVID-19, especially in severe and critical patients, suggests that inflammation is closely related to the development of COVID-19." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "monitoring" } ], "condition": { "id": "DOID:0080600", "recommended_name": { "id": "DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, "synonyms": [ { "id": "DOID:0080600", "name": "SARS-CoV-2 infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan coronavirus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "COVID19", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan seafood market pneumonia virus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019-nCoV infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019 Novel Coronavirus (2019-nCoV)", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" } ] }, "evidence_source": [ { "id": "32677844", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32677844", "evidence_list": [ { "evidence": "Elevated levels of IL-6, D-dimer, CRP, LDH, and ferritin all had an independent increased risk for the clinical outcomes assessed (ICU admission, invasive ventilatory support and death), which were statistically significant." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32296824", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32296824", "evidence_list": [ { "evidence": "We found that old age, and higher serum lactate dehydrogenase, C-reactive protein, the coefficient of variation of red blood cell distribution width, blood urea nitrogen, direct bilirubin, lower albumin, are associated with severe COVID-19." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32161968", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32161968", "evidence_list": [ { "evidence": "LDH and alpha-HBDH may be considerable markers for evaluation of NCOVID-19." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32311826", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32311826", "evidence_list": [ { "evidence": "As would be anticipated, elevation is LDH is common in COVID-19 patients in the ICU setting and indicates a poor outcome." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32048163", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32048163", "evidence_list": [ { "evidence": "Biomarkers that predict the mortality of individual patients more than 10 days in advance with more than 90% accuracy: lactic dehydrogenase (LDH), lymphocyte and high-sensitivity C-reactive protein (hs-CRP). [DOI:10.1038/s42256-020-0180-7] The combinations of the hypoalbuminemia, lymphopenia, and high concentrations of CRP and LDH in 2019-nCoV infected patients upon hospital admission may predict more severe acute lung injury." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32738466", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32738466", "evidence_list": [ { "evidence": "Elevated LDH levels were associated with a ~6-fold increase in odds of developing severe disease and a ~16-fold increase in odds of mortality in patients with COVID-19." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32357994", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32357994", "evidence_list": [ { "evidence": "Post-COVID-19 infection, lower hemoglobin levels, higher total white blood cell (WBC) counts, and higher absolute neutrophil counts were associated with increased mortality. Analysis of other serologic biomarkers demonstrated that elevated D-dimer, lactate, and lactate dehydrogenase (LDH) in patients were significantly correlated with dying." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32259132", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32259132", "evidence_list": [ { "evidence": "Our findings suggest that level of LDH, CRP, ALT and NEU can be used to predict the result of COVID-19 test." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32475810", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32475810", "evidence_list": [ { "evidence": "Serum urea, CREA, CysC, DBIL, CHE and LDH could be used to distinguish severe COVID-19 cases from mild COVID-19 cases. [DOI:10.1101/2020.03.19.20034447] Biomarkers that predict the mortality of individual patients more than 10 days in advance with more than 90% accuracy: lactic dehydrogenase (LDH), lymphocyte and high-sensitivity C-reactive protein (hs-CRP). [DOI:10.1038/s42256-020-0180-7] Since high levels of LDH continued in the ICU patients number of days post-admission, LDH may be a predictive biomarker of severe disease. There is increasing confidence in using LDH as a biomarker to measure severity of COVID-19 infection." }, { "evidence": "C-reactive protein, serum amyloid A, interleukin-6, lactate dehydrogenase, neutrophil-to-lymphocyte ratio, D-dimer, cardiac troponin, and renal biomarkers showed significantly higher levels in patients with severe complications of COVID-19 infection compared to their non-severe counterparts." } ], "tags": [ { "tag": "condition" }, { "tag": "best_biomarker_role" } ] }, { "id": "32589600", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32589600", "evidence_list": [ { "evidence": "Many biomarkers have been associated with poor outcomes and represent a candidate for risk stratification models for predicting severe COVID-19 in order to guide clinical care. Among all, lymphopenia, thrombocytopenia, leucocytosis, CRP, PCT, LDH, AST, ALT, D-dimer, cTn represent the most predictive parameters of severe COVID-19" } ], "tags": [ { "tag": "condition" }, { "tag": "best_biomarker_role" } ] }, { "id": "32596365", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32596365", "evidence_list": [ { "evidence": "The levels of laboratory cardiac markers, lactose dehydrogenase (LDH), creatine kinase (CK), creatinine kinase-muscle/brain activity (CK-MB), myoglobin (Mb), cardiac troponin I (cTnI), alpha-hydroxybutyrate dehydrogenase (α-HBDH), aspartate aminotransferase (AST), and N-terminal of the prohormone brain natriuretic peptide (NT-proBNP) increase in different proportions in patients with COVID-19 (see Table 1)." } ], "tags": [ { "tag": "condition" }, { "tag": "best_biomarker_role" } ] }, { "id": "32209382", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32209382", "evidence_list": [ { "evidence": "This study reveals that the heart is also a major target of COVID-19 infection, and myocardial enzyme spectrum assays could help the diagnosis, prognosis and guide the treatments to prevent heart failure in COVID-19 patients. [DOI:https://doi.org/10.21203/rs.3.rs-23849/v1] We noted significantly increased cTnI, CK, HBDB and LDH levels in very severe group as compare to severe." } ], "tags": [ { "tag": "condition" }, { "tag": "best_biomarker_role" } ] } ], "citation": [ { "title": "The association between biomarkers and clinical outcomes in novel coronavirus pneumonia in a US cohort.", "journal": "Biomarkers in medicine", "authors": "Ayanian S, Reyes J, Lynn L, Teufel K", "date": "2020-07-18", "evidence": [], "reference": [ { "id": "32677844", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32677844" } ] }, { "title": "The role of biomarkers in diagnosis of COVID-19 - A systematic review.", "journal": "Life sciences", "authors": "Kermali M, Khalsa RK, Pillai K, Ismail Z, Harky A", "date": "2020-06-02", "evidence": [], "reference": [ { "id": "32475810", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32475810" } ] }, { "title": "A Tool for Early Prediction of Severe Coronavirus Disease 2019 (COVID-19): A Multicenter Study Using the Risk Nomogram in Wuhan and Guangdong, China.", "journal": "Clinical infectious diseases : an official publication of the Infectious Diseases Society of America", "authors": "Gong J, Ou J, Qiu X, Jie Y, Chen Y, Yuan L, Cao J, Tan M, Xu W, Zheng F, Shi Y, Hu B", "date": "2020-04-17", "evidence": [], "reference": [ { "id": "32296824", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32296824" } ] }, { "title": "A Comparative Study on the Clinical Features of Coronavirus 2019 (COVID-19) Pneumonia With Other Pneumonias.", "journal": "Clinical infectious diseases : an official publication of the Infectious Diseases Society of America", "authors": "Zhao D, Yao F, Wang L, Zheng L, Gao Y, Ye J, Guo F, Zhao H, Gao R", "date": "2020-03-13", "evidence": [], "reference": [ { "id": "32161968", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32161968" } ] }, { "title": "COVID-19 and the clinical hematology laboratory.", "journal": "International journal of laboratory hematology", "authors": "Frater JL, Zini G, d'Onofrio G, Rogers HJ", "date": "2020-04-21", "evidence": [], "reference": [ { "id": "32311826", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32311826" } ] }, { "title": "Clinical and biochemical indexes from 2019-nCoV infected patients linked to viral loads and lung injury.", "journal": "Science China. Life sciences", "authors": "Liu Y, Yang Y, Zhang C, Huang F, Wang F, Yuan J, Wang Z, Li J, Li J, Feng C, Zhang Z, Wang L, Peng L, Chen L, Qin Y, Zhao D, Tan S, Yin L, Xu J, Zhou C, Jiang C, Liu L", "date": "2020-02-13", "evidence": [], "reference": [ { "id": "32048163", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32048163" } ] }, { "title": "Lactate dehydrogenase levels predict coronavirus disease 2019 (COVID-19) severity and mortality: A pooled analysis.", "journal": "The American journal of emergency medicine", "authors": "Henry BM, Aggarwal G, Wong J, Benoit S, Vikse J, Plebani M, Lippi G", "date": "2020-08-02", "evidence": [], "reference": [ { "id": "32738466", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32738466" } ] }, { "title": "Clinical characteristics and outcomes of cancer patients with COVID-19.", "journal": "Journal of medical virology", "authors": "Yang F, Shi S, Zhu J, Shi J, Dai K, Chen X", "date": "2020-05-06", "evidence": [], "reference": [ { "id": "32369209", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32369209" } ] }, { "title": "Case Fatality Rate of Cancer Patients with COVID-19 in a New York Hospital System.", "journal": "Cancer discovery", "authors": "Mehta V, Goel S, Kabarriti R, Cole D, Goldfinger M, Acuna-Villaorduna A, Pradhan K, Thota R, Reissman S, Sparano JA, Gartrell BA, Smith RV, Ohri N, Garg M, Racine AD, Kalnicki S, Perez-Soler R, Halmos B, Verma A", "date": "2020-05-03", "evidence": [], "reference": [ { "id": "32357994", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32357994" } ] }, { "title": "Laboratory Parameters in Detection of COVID-19 Patients with Positive RT-PCR; a Diagnostic Accuracy Study.", "journal": "Archives of academic emergency medicine", "authors": "Mardani R, Ahmadi Vasmehjani A, Zali F, Gholami A, Mousavi Nasab SD, Kaghazian H, Kaviani M, Ahmadi N", "date": "2020-04-08", "evidence": [], "reference": [ { "id": "32259132", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32259132" } ] }, { "title": "Biochemical biomarkers alterations in Coronavirus Disease 2019 (COVID-19).", "journal": "Diagnosis (Berlin, Germany)", "authors": "Ciaccio M, Agnello L", "date": "2020-06-27", "evidence": [], "reference": [ { "id": "32589600", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32589600" } ] }, { "title": "Changes of Laboratory Cardiac Markers and Mechanisms of Cardiac Injury in Coronavirus Disease 2019.", "journal": "BioMed research international", "authors": "Li L, Zhou Q, Xu J", "date": "2020-07-01", "evidence": [], "reference": [ { "id": "32596365", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32596365" } ] }, { "title": "The clinical characteristics of myocardial injury in severe and very severe patients with 2019 novel coronavirus disease.", "journal": "The Journal of infection", "authors": "Zhou B, She J, Wang Y, Ma X", "date": "2020-03-27", "evidence": [], "reference": [ { "id": "32209382", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32209382" } ] } ], "biomarker_canonical_id": "AN6305", "score": 3.8, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 9 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "w": "weight", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6306-1", "biomarker_component": [ { "biomarker": "decreased EOSI count", "assessed_biomarker_entity": { "recommended_name": "Eosinophil", "synonyms": [ { "synonym": "eosinophilic leukocyte" }, { "synonym": "eosinocyte" }, { "synonym": "eosinophilic leucocyte" }, { "synonym": "polymorphonuclear leucocyte" }, { "synonym": "eosinophilic granulocyte" }, { "synonym": "polymorphonuclear leukocyte" } ] }, "assessed_biomarker_entity_id": "CO:CL_0000771", "assessed_entity_type": "cell", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "26449-9" } ], "evidence_source": [ { "id": "32077115", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32077115", "evidence_list": [ { "evidence": "Detailed clinical investigation of 140 hospitalized COVID-19 cases suggests eosinopenia together with lymphopenia may be a potential indicator for diagnosis." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32368728", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32368728", "evidence_list": [ { "evidence": "The combination of eosinopenia and elevated hs-CRP can effectively triage suspected COVID-19 patients from other patients attending the fever clinic with COVID-19-like initial symptoms." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32161940", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32161940", "evidence_list": [ { "evidence": "Severe cases tend to have lower lymphocytes counts, higher leukocyte counts and neutrophil-lymphocyte-ratio (NLR), as well as lower percentages of monocytes, eosinophils, and basophils. Most of severe cases demonstrated elevated levels of infection-related biomarkers and inflammatory cytokines. The number of T cells significantly decreased, and more hampered in severe cases. Both helper T cells and suppressor T cells in patients with COVID-19 were below normal levels, and lower level of helper T cells in severe group. The percentage of naive helper T cells increased and memory helper T cells decreased in severe cases. Patients with COVID-19 also have lower level of regulatory T cells, and more obviously damaged in severe cases." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:0080600", "recommended_name": { "id": "DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, "synonyms": [ { "id": "DOID:0080600", "name": "SARS-CoV-2 infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan coronavirus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "COVID19", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan seafood market pneumonia virus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019-nCoV infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019 Novel Coronavirus (2019-nCoV)", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" } ] }, "evidence_source": [ { "id": "32077115", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32077115", "evidence_list": [ { "evidence": "Detailed clinical investigation of 140 hospitalized COVID-19 cases suggests eosinopenia together with lymphopenia may be a potential indicator for diagnosis." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32368728", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32368728", "evidence_list": [ { "evidence": "The combination of eosinopenia and elevated hs-CRP can effectively triage suspected COVID-19 patients from other patients attending the fever clinic with COVID-19-like initial symptoms." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32161940", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32161940", "evidence_list": [ { "evidence": "Severe cases tend to have lower lymphocytes counts, higher leukocyte counts and neutrophil-lymphocyte-ratio (NLR), as well as lower percentages of monocytes, eosinophils, and basophils. Most of severe cases demonstrated elevated levels of infection-related biomarkers and inflammatory cytokines. The number of T cells significantly decreased, and more hampered in severe cases. Both helper T cells and suppressor T cells in patients with COVID-19 were below normal levels, and lower level of helper T cells in severe group. The percentage of naive helper T cells increased and memory helper T cells decreased in severe cases. Patients with COVID-19 also have lower level of regulatory T cells, and more obviously damaged in severe cases." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Clinical characteristics of 140 patients infected with SARS-CoV-2 in Wuhan, China.", "journal": "Allergy", "authors": "Zhang JJ, Dong X, Cao YY, Yuan YD, Yang YB, Yan YQ, Akdis CA, Gao YD", "date": "2020-02-23", "evidence": [], "reference": [ { "id": "32077115", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32077115" } ] }, { "title": "Eosinopenia and elevated C-reactive protein facilitate triage of COVID-19 patients in fever clinic: A retrospective case-control study.", "journal": "EClinicalMedicine", "authors": "Li Q, Ding X, Xia G, Chen HG, Chen F, Geng Z, Xu L, Lei S, Pan A, Wang L, Wang Z", "date": "2020-05-06", "evidence": [], "reference": [ { "id": "32368728", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32368728" } ] }, { "title": "Dysregulation of Immune Response in Patients With Coronavirus 2019 (COVID-19) in Wuhan, China.", "journal": "Clinical infectious diseases : an official publication of the Infectious Diseases Society of America", "authors": "Qin C, Zhou L, Hu Z, Zhang S, Yang S, Tao Y, Xie C, Ma K, Shang K, Wang W, Tian DS", "date": "2020-03-13", "evidence": [], "reference": [ { "id": "32161940", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32161940" } ] } ], "biomarker_canonical_id": "AN6306", "score": 2.4, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 2 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "c": "condition", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6306-2", "biomarker_component": [ { "biomarker": "decreased EOSI count", "assessed_biomarker_entity": { "recommended_name": "Eosinophil", "synonyms": [ { "synonym": "eosinophilic leukocyte" }, { "synonym": "eosinocyte" }, { "synonym": "eosinophilic leucocyte" }, { "synonym": "polymorphonuclear leucocyte" }, { "synonym": "eosinophilic granulocyte" }, { "synonym": "polymorphonuclear leukocyte" } ] }, "assessed_biomarker_entity_id": "CO:CL_0000771", "assessed_entity_type": "cell", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "26449-9" } ], "evidence_source": [ { "id": "21742945", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/21742945", "evidence_list": [ { "evidence": "In age- and multivariate-adjusted models, eosinophil count was inversely associated with CRC incidence." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_9256" }, "synonyms": [] }, "evidence_source": [ { "id": "21742945", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/21742945", "evidence_list": [ { "evidence": "In age- and multivariate-adjusted models, eosinophil count was inversely associated with CRC incidence." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Inverse association of eosinophil count with colorectal cancer incidence: atherosclerosis risk in communities study.", "journal": "Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology", "authors": "Prizment AE, Anderson KE, Visvanathan K, Folsom AR", "date": "2011-07-12", "evidence": [], "reference": [ { "id": "21742945", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/21742945" } ] } ], "biomarker_canonical_id": "AN6306", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6307-1", "biomarker_component": [ { "biomarker": "increased PLAUR level", "assessed_biomarker_entity": { "recommended_name": "Soluble urokinase plasminogen activator receptor", "synonyms": [ { "synonym": "U-PAR" }, { "synonym": "uPAR" }, { "synonym": "Monocyte activation antigen Mo3" } ] }, "assessed_biomarker_entity_id": "UPKB:Q03405", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "17204-9" } ], "evidence_source": [ { "id": "32354367", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32354367", "evidence_list": [ { "evidence": "A low suPAR level (<4.75 ng/ml) at baseline is a useful biomarker for aiding clinical decisions including discharge of patients presenting with symptoms of COVID-19. [DOI:10.1101/2020.05.27.20114678] Findings suggest that suPAR may early trace patients who need intensified management probably in need of anti-inflammatory treatment." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32613288", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32613288", "evidence_list": [ { "evidence": "In conclusion, suPAR seems extremely promising as a COVID-19 prognostic marker and may assist in the early selection of patients who can stay at home or must be admitted to the hospital and/or intensive care unit. In this difficult outbreak, humanity must use all the available weapons, and suPAR may prove a powerful triage biomarker." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "monitoring" } ], "condition": { "id": "DOID:0080600", "recommended_name": { "id": "DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, "synonyms": [ { "id": "DOID:0080600", "name": "SARS-CoV-2 infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan coronavirus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "COVID19", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan seafood market pneumonia virus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019-nCoV infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019 Novel Coronavirus (2019-nCoV)", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" } ] }, "evidence_source": [ { "id": "32354367", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32354367", "evidence_list": [ { "evidence": "A low suPAR level (<4.75 ng/ml) at baseline is a useful biomarker for aiding clinical decisions including discharge of patients presenting with symptoms of COVID-19. [DOI:10.1101/2020.05.27.20114678] Findings suggest that suPAR may early trace patients who need intensified management probably in need of anti-inflammatory treatment." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32613288", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32613288", "evidence_list": [ { "evidence": "In conclusion, suPAR seems extremely promising as a COVID-19 prognostic marker and may assist in the early selection of patients who can stay at home or must be admitted to the hospital and/or intensive care unit. In this difficult outbreak, humanity must use all the available weapons, and suPAR may prove a powerful triage biomarker." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Soluble urokinase plasminogen activator receptor (suPAR) as an early predictor of severe respiratory failure in patients with COVID-19 pneumonia.", "journal": "Critical care (London, England)", "authors": "Rovina N, Akinosoglou K, Eugen-Olsen J, Hayek S, Reiser J, Giamarellos-Bourboulis EJ", "date": "2020-05-02", "evidence": [], "reference": [ { "id": "32354367", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32354367" } ] }, { "title": "Soluble Urokinase Plasminogen Activator Receptor: A Biomarker for Predicting Complications and Critical Care Admission of COVID-19 Patients.", "journal": "Molecular diagnosis & therapy", "authors": "Chalkias A, Mouzarou A, Samara E, Xanthos T, Ischaki E, Pantazopoulos I", "date": "2020-07-03", "evidence": [], "reference": [ { "id": "32613288", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32613288" } ] } ], "biomarker_canonical_id": "AN6307", "score": 2.2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 1 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "c": "condition", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6307-2", "biomarker_component": [ { "biomarker": "increased PLAUR level", "assessed_biomarker_entity": { "recommended_name": "Soluble urokinase plasminogen activator receptor", "synonyms": [ { "synonym": "U-PAR" }, { "synonym": "uPAR" }, { "synonym": "Monocyte activation antigen Mo3" } ] }, "assessed_biomarker_entity_id": "UPKB:Q03405", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "17204-9" } ], "evidence_source": [ { "id": "9581823", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/9581823", "evidence_list": [ { "evidence": "The median suPAR levels found in each patient group were significantly higher than in the control group. Both ovarian and nonovarian malignant carcinoma subgroups showed a 2-fold increase of suPAR compared to controls. This study shows that the level of the soluble receptor for uPA, a proteinase that is considered to play a key role in physiological and malignant invasion, is increased in serum of a subgroup of ovarian carcinoma patients. Moreover, patients with high suPAR levels showed significantly worse prognosis in survival analysis." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:2394", "recommended_name": { "id": "DOID:2394", "name": "ovarian cancer", "description": "A female reproductive organ cancer that is located_in the ovary.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, "synonyms": [ { "id": "DOID:2394", "name": "primary ovarian cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "tumor of the Ovary", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "ovary neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "malignant tumour of ovary", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "malignant Ovarian tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "ovarian neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" } ] }, "evidence_source": [ { "id": "9581823", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/9581823", "evidence_list": [ { "evidence": "The median suPAR levels found in each patient group were significantly higher than in the control group. Both ovarian and nonovarian malignant carcinoma subgroups showed a 2-fold increase of suPAR compared to controls. This study shows that the level of the soluble receptor for uPA, a proteinase that is considered to play a key role in physiological and malignant invasion, is increased in serum of a subgroup of ovarian carcinoma patients. Moreover, patients with high suPAR levels showed significantly worse prognosis in survival analysis." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "The level of urokinase-type plasminogen activator receptor is increased in serum of ovarian cancer patients.", "journal": "Cancer research", "authors": "Sier CF, Stephens R, Bizik J, Mariani A, Bassan M, Pedersen N, Frigerio L, Ferrari A, Danø K, Brünner N, Blasi F", "date": "1998-05-15", "evidence": [], "reference": [ { "id": "9581823", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/9581823" } ] } ], "biomarker_canonical_id": "AN6307", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "f": "frequency", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6308-1", "biomarker_component": [ { "biomarker": "increased P-SEP level", "assessed_biomarker_entity": { "recommended_name": "Presepsin", "synonyms": [] }, "assessed_biomarker_entity_id": "PRO:PR_000050392", "assessed_entity_type": "peptide", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "32530491", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32530491", "evidence_list": [ { "evidence": "These findings suggest that P-SEP may correlate with lung damage caused by COVID-19 pneumonia and may be useful as a prognostic biomarker for severe COVID-19. Because P-SEP can predict aggravation of ARDS based on laboratory tests on admission, this enables clinicians to identify high-risk COVID-19 patients and determine treatment at an early stage." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:0080600", "recommended_name": { "id": "DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, "synonyms": [ { "id": "DOID:0080600", "name": "SARS-CoV-2 infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan coronavirus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "COVID19", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan seafood market pneumonia virus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019-nCoV infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019 Novel Coronavirus (2019-nCoV)", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" } ] }, "evidence_source": [ { "id": "32530491", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32530491", "evidence_list": [ { "evidence": "These findings suggest that P-SEP may correlate with lung damage caused by COVID-19 pneumonia and may be useful as a prognostic biomarker for severe COVID-19. Because P-SEP can predict aggravation of ARDS based on laboratory tests on admission, this enables clinicians to identify high-risk COVID-19 patients and determine treatment at an early stage." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Presepsin as a predictive biomarker of severity in COVID-19: A case series.", "journal": "Journal of medical virology", "authors": "Fukada A, Kitagawa Y, Matsuoka M, Sakai J, Imai K, Tarumoto N, Orihara Y, Kawamura R, Takeuchi S, Maesaki S, Maeda T", "date": "2020-06-13", "evidence": [], "reference": [ { "id": "32530491", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32530491" } ] } ], "biomarker_canonical_id": "AN6308", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "f": "frequency", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6309-1", "biomarker_component": [ { "biomarker": "increased TNF level", "assessed_biomarker_entity": { "recommended_name": "Tumor necrosis factor alpha", "synonyms": [ { "synonym": "Cachectin" }, { "synonym": "TNF-alpha" }, { "synonym": "Tumor necrosis factor ligand superfamily member 2" }, { "synonym": "TNF-a" } ] }, "assessed_biomarker_entity_id": "UPKB:P01375", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "3074-2" } ], "evidence_source": [ { "id": "32479790", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32479790", "evidence_list": [ { "evidence": "When comparing biochemical indexes of COVID-19 between patients with and without cancer, we found that pro-inflammatory cytokines including TNF-alpha, IL-6, and IL-2R were higher in patients with cancer than in those without cancer." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32382744", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32382744", "evidence_list": [ { "evidence": "The prevalence of severe and complicated cases of COVID-19 is lower in patients in treatment with anti-TNF-alpha than that reported for patients taking steroids." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32511562", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32511562", "evidence_list": [ { "evidence": "COVID-19 is associated with high levels of IL-6, TNF-a, IL-1b, and CXCL8/IL-8. Furthermore, elevated TNF-a, known to contribute to organ damage, was also a strong predictor of poor outcome." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "31986264", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31986264", "evidence_list": [ { "evidence": "Comparison between ICU and non-ICU patients showed that plasma concentrations of IL2, IL7, IL10, GCSF, IP10, MCP1, MIP1A, and TNF alpha were higher in ICU patients than non-ICU patients." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32222466", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32222466", "evidence_list": [ { "evidence": "IL-2, IL-7, IL-10, G-CSF, IP10, MCP1, MIP1A, TNF alpha were higher in severe patients." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:0080600", "recommended_name": { "id": "DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, "synonyms": [ { "id": "DOID:0080600", "name": "SARS-CoV-2 infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan coronavirus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "COVID19", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan seafood market pneumonia virus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019-nCoV infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019 Novel Coronavirus (2019-nCoV)", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" } ] }, "evidence_source": [ { "id": "32479790", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32479790", "evidence_list": [ { "evidence": "When comparing biochemical indexes of COVID-19 between patients with and without cancer, we found that pro-inflammatory cytokines including TNF-alpha, IL-6, and IL-2R were higher in patients with cancer than in those without cancer." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32382744", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32382744", "evidence_list": [ { "evidence": "The prevalence of severe and complicated cases of COVID-19 is lower in patients in treatment with anti-TNF-alpha than that reported for patients taking steroids." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32511562", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32511562", "evidence_list": [ { "evidence": "COVID-19 is associated with high levels of IL-6, TNF-a, IL-1b, and CXCL8/IL-8. Furthermore, elevated TNF-a, known to contribute to organ damage, was also a strong predictor of poor outcome." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "31986264", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31986264", "evidence_list": [ { "evidence": "Comparison between ICU and non-ICU patients showed that plasma concentrations of IL2, IL7, IL10, GCSF, IP10, MCP1, MIP1A, and TNF alpha were higher in ICU patients than non-ICU patients." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32222466", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32222466", "evidence_list": [ { "evidence": "IL-2, IL-7, IL-10, G-CSF, IP10, MCP1, MIP1A, TNF alpha were higher in severe patients." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Clinical characteristics and risk factors associated with COVID-19 disease severity in patients with cancer in Wuhan, China: a multicentre, retrospective, cohort study.", "journal": "The Lancet. Oncology", "authors": "Tian J, Yuan X, Xiao J, Zhong Q, Yang C, Liu B, Cai Y, Lu Z, Wang J, Wang Y, Liu S, Cheng B, Wang J, Zhang M, Wang L, Niu S, Yao Z, Deng X, Zhou F, Wei W, Li Q, Chen X, Chen W, Yang Q, Wu S, Fan J, Shu B, Hu Z, Wang S, Yang XP, Liu W, Miao X, Wang Z", "date": "2020-06-02", "evidence": [], "reference": [ { "id": "32479790", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32479790" } ] }, { "title": "Anti-TNF-α Agents in Inflammatory Bowel Disease and Course of COVID-19.", "journal": "Inflammatory bowel diseases", "authors": "Tursi A, Vetrone LM, Papa A", "date": "2020-05-10", "evidence": [], "reference": [ { "id": "32382744", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32382744" } ] }, { "title": "An inflammatory cytokine signature helps predict COVID-19 severity and death.", "journal": "medRxiv : the preprint server for health sciences", "authors": "Del Valle DM, Kim-Schulze S, Hsin-Hui H, Beckmann ND, Nirenberg S, Wang B, Lavin Y, Swartz T, Madduri D, Stock A, Marron T, Xie H, Patel MK, van Oekelen O, Rahman A, Kovatch P, Aberg J, Schadt E, Jagannath S, Mazumdar M, Charney A, Firpo-Betancourt A, Mendu DR, Jhang J, Reich D, Sigel K, Cordon-Cardo C, Feldmann M, Parekh S, Merad M, Gnjatic S", "date": "2020-06-09", "evidence": [], "reference": [ { "id": "32511562", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32511562" } ] }, { "title": "Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China.", "journal": "Lancet (London, England)", "authors": "Huang C, Wang Y, Li X, Ren L, Zhao J, Hu Y, Zhang L, Fan G, Xu J, Gu X, Cheng Z, Yu T, Xia J, Wei Y, Wu W, Xie X, Yin W, Li H, Liu M, Xiao Y, Gao H, Guo L, Xie J, Wang G, Jiang R, Gao Z, Jin Q, Wang J, Cao B", "date": "2020-01-28", "evidence": [], "reference": [ { "id": "31986264", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31986264" } ] }, { "title": "The use of anti-inflammatory drugs in the treatment of people with severe coronavirus disease 2019 (COVID-19): The Perspectives of clinical immunologists from China.", "journal": "Clinical immunology (Orlando, Fla.)", "authors": "Zhang W, Zhao Y, Zhang F, Wang Q, Li T, Liu Z, Wang J, Qin Y, Zhang X, Yan X, Zeng X, Zhang S", "date": "2020-03-31", "evidence": [], "reference": [ { "id": "32222466", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32222466" } ] } ], "biomarker_canonical_id": "AN6309", "score": 2.8, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 4 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6309-2", "biomarker_component": [ { "biomarker": "increased TNF level", "assessed_biomarker_entity": { "recommended_name": "Tumor necrosis factor alpha", "synonyms": [ { "synonym": "Cachectin" }, { "synonym": "TNF-alpha" }, { "synonym": "Tumor necrosis factor ligand superfamily member 2" }, { "synonym": "TNF-a" } ] }, "assessed_biomarker_entity_id": "UPKB:P01375", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "3074-2" } ], "evidence_source": [ { "id": "24481866", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/24481866", "evidence_list": [ { "evidence": "Elevated levels of TNF-alpha were found in patients with head and neck squamous cell carcinoma (HNSCC). An upregulated TNF-alpha, in combination with CRP, was significantly related to shorter patient survival, independent of clinical stage. Findings indicate that TNF-alpha might be suitable as biomarkers in combination with tumor TNM staging for predicting survival and individualized treatment." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:11934", "recommended_name": { "id": "DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11934" }, "synonyms": [ { "id": "DOID:11934", "name": "head and neck neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11934" }, { "id": "DOID:11934", "name": "head/neck neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11934" }, { "id": "DOID:11934", "name": "head and neck tumours", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11934" }, { "id": "DOID:11934", "name": "tumor of head and neck", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11934" } ] }, "evidence_source": [ { "id": "24481866", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/24481866", "evidence_list": [ { "evidence": "Elevated levels of TNF-alpha were found in patients with head and neck squamous cell carcinoma (HNSCC). An upregulated TNF-alpha, in combination with CRP, was significantly related to shorter patient survival, independent of clinical stage. Findings indicate that TNF-alpha might be suitable as biomarkers in combination with tumor TNM staging for predicting survival and individualized treatment." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Plasma tumor necrosis factor-α and C-reactive protein as biomarker for survival in head and neck squamous cell carcinoma.", "journal": "Journal of cancer research and clinical oncology", "authors": "Andersson BÅ, Lewin F, Lundgren J, Nilsson M, Rutqvist LE, Löfgren S, Laytragoon-Lewin N", "date": "2014-02-01", "evidence": [], "reference": [ { "id": "24481866", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/24481866" } ] } ], "biomarker_canonical_id": "AN6309", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6310-1", "biomarker_component": [ { "biomarker": "increased TMPRSS2 level", "assessed_biomarker_entity": { "recommended_name": "Transmembrane protease serine 2", "synonyms": [ { "synonym": "Serine protease 10" } ] }, "assessed_biomarker_entity_id": "UPKB:O15393", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "32437018", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32437018", "evidence_list": [ { "evidence": "The role of transmembrane protease serine 2 (TMPRSS2) as a contributing factor to the more severe outcomes noted for COVID-19. Validated TMPRSS2 SNPs that are confirmed to be predictive biomarkers can be incorporated in the CDCs current list of clinical biomarkers for disease severity as discussed above." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32660890", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32660890", "evidence_list": [ { "evidence": "TMPRSS2 expression is regulated in part by androgens and is a known biomarker of prostate cancer severity when fused with ERG. It is known that TMPRSS2 expression is upregulated by androgens in prostate cancer cell lines and in vivo. The authors analyzed data from 4,532 men who tested positive for SARS-CoV-2. Of these patients, 430 (9.5%) had cancer and 118 (2.6%) had prostate cancer (28% of all cancers). Consistent with other publications, men with cancer have worse disease presentations than men without cancer, even when stratified for age. In the 5,273 prostate cancer patients on androgen deprivation therapy (ADT); only four of these patients were positive for SARS-CoV-2. The authors stated that men positive for SARS-CoV-2 and on ADT not only had improved outcomes over other men with prostate cancer positive for SARS-CoV-2, but that ADT may have reduced the chance of infection. They concluded that ADT had a protective effect in men positive for SARS-CoV-2 infection. ADT therapy provides the first evidence that reducing androgens or their effect on tissues may have a beneficial impact on outcomes in men infected with SARS-CoV-2." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:0080600", "recommended_name": { "id": "DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, "synonyms": [ { "id": "DOID:0080600", "name": "SARS-CoV-2 infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan coronavirus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "COVID19", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan seafood market pneumonia virus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019-nCoV infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019 Novel Coronavirus (2019-nCoV)", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" } ] }, "evidence_source": [ { "id": "32437018", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32437018", "evidence_list": [ { "evidence": "The role of transmembrane protease serine 2 (TMPRSS2) as a contributing factor to the more severe outcomes noted for COVID-19. Validated TMPRSS2 SNPs that are confirmed to be predictive biomarkers can be incorporated in the CDCs current list of clinical biomarkers for disease severity as discussed above." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32660890", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32660890", "evidence_list": [ { "evidence": "TMPRSS2 expression is regulated in part by androgens and is a known biomarker of prostate cancer severity when fused with ERG. It is known that TMPRSS2 expression is upregulated by androgens in prostate cancer cell lines and in vivo. The authors analyzed data from 4,532 men who tested positive for SARS-CoV-2. Of these patients, 430 (9.5%) had cancer and 118 (2.6%) had prostate cancer (28% of all cancers). Consistent with other publications, men with cancer have worse disease presentations than men without cancer, even when stratified for age. In the 5,273 prostate cancer patients on androgen deprivation therapy (ADT); only four of these patients were positive for SARS-CoV-2. The authors stated that men positive for SARS-CoV-2 and on ADT not only had improved outcomes over other men with prostate cancer positive for SARS-CoV-2, but that ADT may have reduced the chance of infection. They concluded that ADT had a protective effect in men positive for SARS-CoV-2 infection. ADT therapy provides the first evidence that reducing androgens or their effect on tissues may have a beneficial impact on outcomes in men infected with SARS-CoV-2." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "TMPRSS2: Potential Biomarker for COVID-19 Outcomes.", "journal": "Journal of clinical pharmacology", "authors": "Strope JD, PharmD CHC, Figg WD", "date": "2020-05-22", "evidence": [], "reference": [ { "id": "32437018", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32437018" } ] }, { "title": "Are sex discordant outcomes in COVID-19 related to sex hormones?", "journal": "Seminars in oncology", "authors": "Strope JD, Chau CH, Figg WD", "date": "2020-07-15", "evidence": [], "reference": [ { "id": "32660890", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32660890" } ] } ], "biomarker_canonical_id": "AN6310", "score": 1.2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 1 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "f": "frequency", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6311-1", "biomarker_component": [ { "biomarker": "increased ACE2 level", "assessed_biomarker_entity": { "recommended_name": "Angiotensin-converting enzyme 2", "synonyms": [ { "synonym": "Angiotensin-converting enzyme homolog" }, { "synonym": "ACEH" }, { "synonym": "Angiotensin-converting enzyme-related carboxypeptidase" }, { "synonym": "ACE-related carboxypeptidase" }, { "synonym": "Metalloprotease MPROT15" } ] }, "assessed_biomarker_entity_id": "UPKB:Q9BYF1", "assessed_entity_type": "protein", "specimen": [ { "name": "lung", "id": "UBERON:0002048", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0002048", "loinc_code": "" } ], "evidence_source": [ { "id": "32916258", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32916258", "evidence_list": [ { "evidence": "Our study showed an increased rate of expression of ACE2 in an elderly male patient in the age group of 60-70 who has LAUD or LUSC. We also conducted a prognostic analysis of ACE2 in lung cancer, we found that ACE2 mRNA is highly expressed. High expression of ACE2 may lead to higher susceptibility of lung cancer patient towards COVID 19 and ACE2 can serve as the best potential biomarker for this disease compared to co-expressed genes." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0002048" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "name": "COVID-19", "description": "A respiratory system cancer that is located_in the lung.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1324" }, "synonyms": [] }, "evidence_source": [ { "id": "32916258", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32916258", "evidence_list": [ { "evidence": "Our study showed an increased rate of expression of ACE2 in an elderly male patient in the age group of 60-70 who has LAUD or LUSC. We also conducted a prognostic analysis of ACE2 in lung cancer, we found that ACE2 mRNA is highly expressed. High expression of ACE2 may lead to higher susceptibility of lung cancer patient towards COVID 19 and ACE2 can serve as the best potential biomarker for this disease compared to co-expressed genes." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Identification of angiotensin-converting enzyme 2 (ACE2) protein as the potential biomarker in SARS-CoV-2 infection-related lung cancer using computational analyses.", "journal": "Genomics", "authors": "Samad A, Jafar T, Rafi JH", "date": "2020-09-12", "evidence": [], "reference": [ { "id": "32916258", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32916258" } ] } ], "biomarker_canonical_id": "AN6311", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "c": "condition", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6311-2", "biomarker_component": [ { "biomarker": "increased ACE2 level", "assessed_biomarker_entity": { "recommended_name": "Angiotensin-converting enzyme 2", "synonyms": [ { "synonym": "Angiotensin-converting enzyme homolog" }, { "synonym": "ACEH" }, { "synonym": "Angiotensin-converting enzyme-related carboxypeptidase" }, { "synonym": "ACE-related carboxypeptidase" }, { "synonym": "Metalloprotease MPROT15" } ] }, "assessed_biomarker_entity_id": "UPKB:Q9BYF1", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "32698840", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32698840", "evidence_list": [ { "evidence": "sACE2 levels showed reliable associations with all individuals components of Metabolic Syndrome. This profile of associations was statistically significantly stronger in men, compared to women, and suggests that preexisting cardiometabolic conditions might confer increased severity of symptoms in some COVID-19 patients through increased expression of ACE2 in the liver." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "monitoring" } ], "condition": { "id": "DOID:0080600", "recommended_name": { "id": "DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, "synonyms": [ { "id": "DOID:0080600", "name": "SARS-CoV-2 infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan coronavirus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "COVID19", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan seafood market pneumonia virus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019-nCoV infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019 Novel Coronavirus (2019-nCoV)", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" } ] }, "evidence_source": [ { "id": "32698840", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32698840", "evidence_list": [ { "evidence": "sACE2 levels showed reliable associations with all individuals components of Metabolic Syndrome. This profile of associations was statistically significantly stronger in men, compared to women, and suggests that preexisting cardiometabolic conditions might confer increased severity of symptoms in some COVID-19 patients through increased expression of ACE2 in the liver." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Plasma levels of soluble ACE2are associated with sex, Metabolic Syndrome, and its biomarkers in a large cohort, pointing to a possible mechanism for increased severity in COVID-19.", "journal": "Critical care (London, England)", "authors": "Kornilov SA, Lucas I, Jade K, Dai CL, Lovejoy JC, Magis AT", "date": "2020-07-24", "evidence": [], "reference": [ { "id": "32698840", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32698840" } ] } ], "biomarker_canonical_id": "AN6311", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "c": "condition", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6312-1", "biomarker_component": [ { "biomarker": "decreased ACE2 level", "assessed_biomarker_entity": { "recommended_name": "Angiotensin-converting enzyme 2", "synonyms": [ { "synonym": "Angiotensin-converting enzyme homolog" }, { "synonym": "ACEH" }, { "synonym": "Angiotensin-converting enzyme-related carboxypeptidase" }, { "synonym": "ACE-related carboxypeptidase" }, { "synonym": "Metalloprotease MPROT15" } ] }, "assessed_biomarker_entity_id": "UPKB:Q9BYF1", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "32339157", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32339157", "evidence_list": [ { "evidence": "Expression of ACE2 decreased in vivo and in vitro after SARS-CoV infection. Tumor tissues may be more susceptible to SARS-CoV-2 infection in COVID-19 patients with UCEC (Uterine Corpus Endometrial Carcinoma) and KIRP (Kidney Renal Papillary Cell Carcinoma), which may worsen the prognosis." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:0080600", "recommended_name": { "id": "DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, "synonyms": [ { "id": "DOID:0080600", "name": "SARS-CoV-2 infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan coronavirus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "COVID19", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan seafood market pneumonia virus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019-nCoV infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019 Novel Coronavirus (2019-nCoV)", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" } ] }, "evidence_source": [ { "id": "32339157", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32339157", "evidence_list": [ { "evidence": "Expression of ACE2 decreased in vivo and in vitro after SARS-CoV infection. Tumor tissues may be more susceptible to SARS-CoV-2 infection in COVID-19 patients with UCEC (Uterine Corpus Endometrial Carcinoma) and KIRP (Kidney Renal Papillary Cell Carcinoma), which may worsen the prognosis." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "ACE2 correlated with immune infiltration serves as a prognostic biomarker in endometrial carcinoma and renal papillary cell carcinoma: implication for COVID-19.", "journal": "Aging", "authors": "Yang J, Li H, Hu S, Zhou Y", "date": "2020-04-28", "evidence": [], "reference": [ { "id": "32339157", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32339157" } ] } ], "biomarker_canonical_id": "AN6312", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "w": "weight", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6313-1", "biomarker_component": [ { "biomarker": "decreased ACE2 level", "assessed_biomarker_entity": { "recommended_name": "Angiotensin-converting enzyme 2", "synonyms": [ { "synonym": "ACEH" } ] }, "assessed_biomarker_entity_id": "NCBI: 59272", "assessed_entity_type": "gene", "specimen": [ { "name": "pancreas", "id": "UBERON:0001264", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0001264", "loinc_code": "" } ], "evidence_source": [ { "id": "19212105", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/19212105", "evidence_list": [ { "evidence": "Expression of ACE2 is decreased in pancreatic ductal adenocarcinoma tissues. The reduction of ACE2 expression by RNA interference promoted the proliferation of cultured pancreatic cancer cells. It was found that ANGII (angiotensin II, a biologically active peptide that works as a regulator of cardiovasular homeostasist) contributes to the down-regulation of ACE2 in cancer patients." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0001264" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:1793", "recommended_name": { "id": "DOID:1793", "name": "pancreatic cancer", "description": "An endocrine gland cancer located_in the pancreas.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, "synonyms": [ { "id": "DOID:1793", "name": "Ca head of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "Ca body of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "pancreatic tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "malignant neoplasm of tail of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "malignant neoplasm of head of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "pancreatic neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "Ca tail of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "pancreas neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "malignant neoplasm of body of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" } ] }, "evidence_source": [ { "id": "19212105", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/19212105", "evidence_list": [ { "evidence": "Expression of ACE2 is decreased in pancreatic ductal adenocarcinoma tissues. The reduction of ACE2 expression by RNA interference promoted the proliferation of cultured pancreatic cancer cells. It was found that ANGII (angiotensin II, a biologically active peptide that works as a regulator of cardiovasular homeostasist) contributes to the down-regulation of ACE2 in cancer patients." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Decreased expression of angiotensin-converting enzyme 2 in pancreatic ductal adenocarcinoma is associated with tumor progression.", "journal": "The Tohoku journal of experimental medicine", "authors": "Zhou L, Zhang R, Yao W, Wang J, Qian A, Qiao M, Zhang Y, Yuan Y", "date": "2009-02-13", "evidence": [], "reference": [ { "id": "19212105", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/19212105" } ] } ], "biomarker_canonical_id": "AN6313", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6314-1", "biomarker_component": [ { "biomarker": "increased WFDC2 level", "assessed_biomarker_entity": { "recommended_name": "WAP four-disulfide core domain protein 2", "synonyms": [ { "synonym": "Epididymal secretory protein E4" }, { "synonym": "Major epididymis-specific protein E4" }, { "synonym": "Putative protease inhibitor WAP5" } ] }, "assessed_biomarker_entity_id": "UPKB:Q14508", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "55180-4" } ], "evidence_source": [ { "id": "21633297", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/21633297", "evidence_list": [ { "evidence": "Early diagnosis is the most important determinant of early survival for ovarian cancer, and increased levels of HE4, in combination with CA125, is used as a diagnostic marker for ovarian cancer. HE4 levels were found to be significantly higher in individuals with ovarian cancer. Combining both HE4 and CA125 yielded specificity for ovarian cancer of 100%." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "19732003", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/19732003", "evidence_list": [ { "evidence": "Preliminary data show that HE4 may have more potential than cancer antigen 125 in discriminating benign from cancerous ovarian masses, and has the strongest correlation with endometrial cancer of all markers tested to date. Utilizing risk stratification, a panel of biomarkers including HE4 may ultimately be useful for detecting ovarian and endometrial cancer at an early stage in patients at high risk." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:2394", "recommended_name": { "id": "DOID:2394", "name": "ovarian cancer", "description": "A female reproductive organ cancer that is located_in the ovary.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, "synonyms": [ { "id": "DOID:2394", "name": "primary ovarian cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "tumor of the Ovary", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "ovary neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "malignant tumour of ovary", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "malignant Ovarian tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "ovarian neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" } ] }, "evidence_source": [ { "id": "21633297", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/21633297", "evidence_list": [ { "evidence": "Early diagnosis is the most important determinant of early survival for ovarian cancer, and increased levels of HE4, in combination with CA125, is used as a diagnostic marker for ovarian cancer. HE4 levels were found to be significantly higher in individuals with ovarian cancer. Combining both HE4 and CA125 yielded specificity for ovarian cancer of 100%." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "19732003", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/19732003", "evidence_list": [ { "evidence": "Preliminary data show that HE4 may have more potential than cancer antigen 125 in discriminating benign from cancerous ovarian masses, and has the strongest correlation with endometrial cancer of all markers tested to date. Utilizing risk stratification, a panel of biomarkers including HE4 may ultimately be useful for detecting ovarian and endometrial cancer at an early stage in patients at high risk." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Human epididymis protein 4 (HE4) as a serum tumor biomarker in patients with ovarian carcinoma.", "journal": "International journal of gynecological cancer : official journal of the International Gynecological Cancer Society", "authors": "Chang X, Ye X, Dong L, Cheng H, Cheng Y, Zhu L, Liao Q, Zhao Y, Tian L, Fu T, Chen J, Cui H", "date": "2011-06-03", "evidence": [], "reference": [ { "id": "21633297", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/21633297" } ] }, { "title": "HE4 as a biomarker for ovarian and endometrial cancer management.", "journal": "Expert review of molecular diagnostics", "authors": "Li J, Dowdy S, Tipton T, Podratz K, Lu WG, Xie X, Jiang SW", "date": "2009-09-08", "evidence": [], "reference": [ { "id": "19732003", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/19732003" } ] } ], "biomarker_canonical_id": "AN6314", "score": 2.2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 1 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "c": "condition", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6314-2", "biomarker_component": [ { "biomarker": "increased WFDC2 level", "assessed_biomarker_entity": { "recommended_name": "WAP four-disulfide core domain protein 2", "synonyms": [ { "synonym": "Epididymal secretory protein E4" }, { "synonym": "Major epididymis-specific protein E4" }, { "synonym": "Putative protease inhibitor WAP5" } ] }, "assessed_biomarker_entity_id": "UPKB:Q14508", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "55180-4" } ], "evidence_source": [ { "id": "32347972", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32347972", "evidence_list": [ { "evidence": "This is the first report with such a substantial evaluation of cancer biomarkers on a large patient population of COVID-19. Our data demonstrate that levels of serum HE4, CYFRA21-1, CEA, CA125, CA153, SCC, and NSE are positively associated with CRP, a crucial factor in correlation with the severity of the disease. We concluded that elevations of serum cancer biomarkers positively correlated with the pathological progressions of COVID-19, demonstrating diffuse and acute pathophysiological injuries in COVID-19." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32347972", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32347972", "evidence_list": [ { "evidence": "Increases in levels of Human epididymis protein 4 (HE4), Cytokeratin-19 fragment (CYFRA21-1) Carcinoembryonic antigen (CEA), Carbohydrate antigen 125 (CA125), Carbohydrate antigen 153 (CA153), Squamous cell carcinoma antigen (SCC), Carbohydrate antigen 199 (CA199). There were positive associations between levels of C-reactive protein and levels of HE4 (R= 0.631, p<0.001), CYFRA21-1 (R= 0.431, p<0.001), CEA (R= 0.316, p<0.001), SCC (R= 0.351, p<0.001), CA153 (R= 0.359, p<0.001) and CA125 (R= 0.223, p=0.031). We concluded that elevations of serum cancer biomarkers positively correlated with the pathological progressions of COVID-19, demonstrating diffuse and acute lung injuries." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32347972", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32347972", "evidence_list": [ { "evidence": "Significant increases in levels of human epididymis protein 4 (HE4), cytokeratin-19 fragment (CYFRA21-1), carcinoembryonic antigen (CEA), carbohydrate antigens (CA) 125 , and 153. Squamous cell carcinoma antigen (SCC) and CA199 increased significantly." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32347972", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32347972", "evidence_list": [ { "evidence": "Presence of elevated HE4 levels shown as predictor of COVID-19 severity." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:0080600", "recommended_name": { "id": "DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, "synonyms": [ { "id": "DOID:0080600", "name": "SARS-CoV-2 infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan coronavirus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "COVID19", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan seafood market pneumonia virus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019-nCoV infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019 Novel Coronavirus (2019-nCoV)", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" } ] }, "evidence_source": [ { "id": "32347972", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32347972", "evidence_list": [ { "evidence": "This is the first report with such a substantial evaluation of cancer biomarkers on a large patient population of COVID-19. Our data demonstrate that levels of serum HE4, CYFRA21-1, CEA, CA125, CA153, SCC, and NSE are positively associated with CRP, a crucial factor in correlation with the severity of the disease. We concluded that elevations of serum cancer biomarkers positively correlated with the pathological progressions of COVID-19, demonstrating diffuse and acute pathophysiological injuries in COVID-19." }, { "evidence": "Increases in levels of Human epididymis protein 4 (HE4), Cytokeratin-19 fragment (CYFRA21-1) Carcinoembryonic antigen (CEA), Carbohydrate antigen 125 (CA125), Carbohydrate antigen 153 (CA153), Squamous cell carcinoma antigen (SCC), Carbohydrate antigen 199 (CA199). There were positive associations between levels of C-reactive protein and levels of HE4 (R= 0.631, p<0.001), CYFRA21-1 (R= 0.431, p<0.001), CEA (R= 0.316, p<0.001), SCC (R= 0.351, p<0.001), CA153 (R= 0.359, p<0.001) and CA125 (R= 0.223, p=0.031). We concluded that elevations of serum cancer biomarkers positively correlated with the pathological progressions of COVID-19, demonstrating diffuse and acute lung injuries." }, { "evidence": "Significant increases in levels of human epididymis protein 4 (HE4), cytokeratin-19 fragment (CYFRA21-1), carcinoembryonic antigen (CEA), carbohydrate antigens (CA) 125 , and 153. Squamous cell carcinoma antigen (SCC) and CA199 increased significantly." }, { "evidence": "Presence of elevated HE4 levels shown as predictor of COVID-19 severity." } ], "tags": [ { "tag": "condition" }, { "tag": "best_biomarker_role" } ] } ], "citation": [ { "title": "Elevations of serum cancer biomarkers correlate with severity of COVID-19.", "journal": "Journal of medical virology", "authors": "Wei X, Su J, Yang K, Wei J, Wan H, Cao X, Tan W, Wang H", "date": "2020-04-30", "evidence": [], "reference": [ { "id": "32347972", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32347972" } ] } ], "biomarker_canonical_id": "AN6314", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "c": "condition", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6314-3", "biomarker_component": [ { "biomarker": "increased WFDC2 level", "assessed_biomarker_entity": { "recommended_name": "WAP four-disulfide core domain protein 2", "synonyms": [ { "synonym": "Epididymal secretory protein E4" }, { "synonym": "Major epididymis-specific protein E4" }, { "synonym": "Putative protease inhibitor WAP5" } ] }, "assessed_biomarker_entity_id": "UPKB:Q14508", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "55180-4" } ], "evidence_source": [ { "id": "27446579", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/27446579", "evidence_list": [ { "evidence": "There was a significant difference in the median serum levels of HE4 in breast cancer patients, ovarian cancer patients and healthy volunteers (14.63, 16.47 and 11.52 pmol/l, respectively; P=0.013). No significant differences between the breast cancer and ovarian cancer patient groups was observed, the median serum levels of HE4 in these groups were significantly higher than those in the healthy volunteer group (P=0.006 and P=0.017, respectively).The cutoff value for the prediction of breast cancer was determined at >13.24 pmol/l for HE4 with a sensitivity of 61.11%, specificity of 68.75%, positive predictive value of 81.48%, negative predictive value of 44.0% and accuracy of 63.46% [AUC, 0.740 (95% CI, 0.604‚Äì0.875), P=0.006] A significant elevation of serum HE4 levels in patients with breast cancer compared with that in healthy controls was identified. HE4 may serve as a novel biomarker for the diagnosis of breast cancer." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "name": "breast cancer", "description": "A thoracic cancer that originates in the mammary gland.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, "synonyms": [ { "id": "DOID:1612", "name": "malignant tumor of the breast", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "breast tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "mammary cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "primary breast cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "mammary tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "malignant neoplasm of breast", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" } ] }, "evidence_source": [ { "id": "27446579", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/27446579", "evidence_list": [ { "evidence": "There was a significant difference in the median serum levels of HE4 in breast cancer patients, ovarian cancer patients and healthy volunteers (14.63, 16.47 and 11.52 pmol/l, respectively; P=0.013). No significant differences between the breast cancer and ovarian cancer patient groups was observed, the median serum levels of HE4 in these groups were significantly higher than those in the healthy volunteer group (P=0.006 and P=0.017, respectively).The cutoff value for the prediction of breast cancer was determined at >13.24 pmol/l for HE4 with a sensitivity of 61.11%, specificity of 68.75%, positive predictive value of 81.48%, negative predictive value of 44.0% and accuracy of 63.46% [AUC, 0.740 (95% CI, 0.604‚Äì0.875), P=0.006] A significant elevation of serum HE4 levels in patients with breast cancer compared with that in healthy controls was identified. HE4 may serve as a novel biomarker for the diagnosis of breast cancer." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "A new marker for breast cancer diagnosis, human epididymis protein 4: A preliminary study.", "journal": "Molecular and clinical oncology", "authors": "Gündüz UR, Gunaldi M, Isiksacan N, Gündüz S, Okuturlar Y, Kocoglu H", "date": "2016-07-23", "evidence": [], "reference": [ { "id": "27446579", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/27446579" } ] } ], "biomarker_canonical_id": "AN6314", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "f": "frequency", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6315-1", "biomarker_component": [ { "biomarker": "increased KRT19 level", "assessed_biomarker_entity": { "recommended_name": "Cytokeratin-19 fragment", "synonyms": [ { "synonym": "Cytokeratin-19" }, { "synonym": "CK-19" }, { "synonym": "Keratin-19" }, { "synonym": "K19" } ] }, "assessed_biomarker_entity_id": "UPKB:P08727", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "16033098", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/16033098", "evidence_list": [ { "evidence": "Tumor marker serum levels were related to histological type and tumor extension, with ProGRP being the most sensitive marker in SCLC, CEA in adenocarcinomas and CYFRA 21-1 in squamous tumors. The most sensitive combinations of tumor markers were ProGRP and NSE in SCLC (88%), and CEA plus CYFRA in NSCLC (82%). In summary, ProGRP is the tumor marker of choice in SCLC and NSE is a complementary tumor marker in this histological type." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "7541742", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/7541742", "evidence_list": [ { "evidence": "Cyfra 21-1 levels were significantly higher in advanced NSCLC than in early-stage disease. All 29 patients with serum concentrations > 32 ng/mL had stage IIIB-IV and only one of 14 patients with stage I-II disease had Cyfra 21-1 level > 18 ng/mL. In the multivariate analysis of survival, Cyfra 21-1 was an independent prognostic factor along with performance status and disease stage in NSCLC. Cyfra 21-1 is a sensitive and specific tumor marker of NSCLC, especially of squamous cell subtype. It also reflects the extent of the disease and has an independent prognostic role along with performance status and disease stage in NSCLC. Cyfra 21-1 was an independent prognostic factor along with performance status and disease stage in NSCLC." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1324" }, "synonyms": [] }, "evidence_source": [ { "id": "16033098", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/16033098", "evidence_list": [ { "evidence": "Tumor marker serum levels were related to histological type and tumor extension, with ProGRP being the most sensitive marker in SCLC, CEA in adenocarcinomas and CYFRA 21-1 in squamous tumors. The most sensitive combinations of tumor markers were ProGRP and NSE in SCLC (88%), and CEA plus CYFRA in NSCLC (82%). In summary, ProGRP is the tumor marker of choice in SCLC and NSE is a complementary tumor marker in this histological type." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "7541742", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/7541742", "evidence_list": [ { "evidence": "Cyfra 21-1 levels were significantly higher in advanced NSCLC than in early-stage disease. All 29 patients with serum concentrations > 32 ng/mL had stage IIIB-IV and only one of 14 patients with stage I-II disease had Cyfra 21-1 level > 18 ng/mL. In the multivariate analysis of survival, Cyfra 21-1 was an independent prognostic factor along with performance status and disease stage in NSCLC. Cyfra 21-1 is a sensitive and specific tumor marker of NSCLC, especially of squamous cell subtype. It also reflects the extent of the disease and has an independent prognostic role along with performance status and disease stage in NSCLC. Cyfra 21-1 was an independent prognostic factor along with performance status and disease stage in NSCLC." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Pro-gastrin-releasing peptide (proGRP) in patients with benign and malignant diseases: comparison with CEA, SCC, CYFRA 21-1 and NSE in patients with lung cancer.", "journal": "Anticancer research", "authors": "Molina R, Auge JM, Filella X, Viñolas N, Alicarte J, Domingo JM, Ballesta AM", "date": "2005-07-22", "evidence": [], "reference": [ { "id": "16033098", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/16033098" } ] }, { "title": "Cyfra 21-1 as a biologic marker of non-small cell lung cancer. Evaluation of sensitivity, specificity, and prognostic role.", "journal": "Chest", "authors": "Wieskopf B, Demangeat C, Purohit A, Stenger R, Gries P, Kreisman H, Quoix E", "date": "1995-07-01", "evidence": [], "reference": [ { "id": "7541742", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/7541742" } ] } ], "biomarker_canonical_id": "AN6315", "score": 1.4, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 2 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "c": "condition", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6315-2", "biomarker_component": [ { "biomarker": "increased KRT19 level", "assessed_biomarker_entity": { "recommended_name": "Cytokeratin-19 fragment", "synonyms": [ { "synonym": "Cytokeratin-19" }, { "synonym": "CK-19" }, { "synonym": "Keratin-19" }, { "synonym": "K19" } ] }, "assessed_biomarker_entity_id": "UPKB:P08727", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "32347972", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32347972", "evidence_list": [ { "evidence": "This is the first report with such a substantial evaluation of cancer biomarkers on a large patient population of COVID-19. Our data demonstrate that levels of serum HE4, CYFRA21-1, CEA, CA125, CA153, SCC, and NSE are positively associated with CRP, a crucial factor in correlation with the severity of the disease. We concluded that elevations of serum cancer biomarkers positively correlated with the pathological progressions of COVID-19, demonstrating diffuse and acute pathophysiological injuries in COVID-19." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32347972", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32347972", "evidence_list": [ { "evidence": "Increases in levels of Human epididymis protein 4 (HE4), Cytokeratin-19 fragment (CYFRA21-1) Carcinoembryonic antigen (CEA), Carbohydrate antigen 125 (CA125), Carbohydrate antigen 153 (CA153), Squamous cell carcinoma antigen (SCC), Carbohydrate antigen 199 (CA199). There were positive associations between levels of C-reactive protein and levels of HE4 (R= 0.631, p<0.001), CYFRA21-1 (R= 0.431, p<0.001), CEA (R= 0.316, p<0.001), SCC (R= 0.351, p<0.001), CA153 (R= 0.359, p<0.001) and CA125 (R= 0.223, p=0.031). We concluded that elevations of serum cancer biomarkers positively correlated with the pathological progressions of COVID-19, demonstrating diffuse and acute lung injuries." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32504736", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32504736", "evidence_list": [ { "evidence": "In short, we concluded that the concentrations of tumor biomarkers of CEA, CYFRA21-1, NSE, SCCA, ProGRP were elevated in COVID-19 patients, and that CEA, CYFRA21-1, SCCA could predict the clinical outcome of COVID-19 patients." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32347972", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32347972", "evidence_list": [ { "evidence": "Significant increases in levels of human epididymis protein 4 (HE4), cytokeratin-19 fragment (CYFRA21-1), carcinoembryonic antigen (CEA), carbohydrate antigens (CA) 125 , and 153 Squamous cell carcinoma antigen (SCC) and CA199 increased significantly." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32347972", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32347972", "evidence_list": [ { "evidence": "Presence of elevated CYFRA21 levels shown as predictor of COVID-19 severity." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32504736", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32504736", "evidence_list": [ { "evidence": "Increased levels of CYFRA21-1 were observed in COVID-19 patients, and could predict the clinical outcome of patients." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32347972", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32347972", "evidence_list": [ { "evidence": "Additional cancer biomarkers such as carcinoembryonic antigen (CEA), carbohydrate antigens 125 and 153, squamous cell carcinoma antigen (SCC) and neuron-specific enolase (NSE) increased significantly in many critical cases. [DOI:10.2139/ssrn.3552854] Increases in levels of Human epididymis protein 4 (HE4), Cytokeratin-19 fragment (CYFRA21-1) Carcinoembryonic antigen (CEA), Carbohydrate antigen 125 (CA125), Carbohydrate antigen 153 (CA153), Squamous cell carcinoma antigen (SCC), Carbohydrate antigen 199 (CA199). There were positive associations between levels of C-reactive protein and levels of HE4 (R= 0.631, p<0.001), CYFRA21-1(R= 0.431, p<0.001), CEA (R= 0.316, p<0.001), SCC (R= 0.351, p<0.001), CA153 (R= 0.359, p<0.001) and CA125 (R= 0.223, p=0.031). We concluded that elevations of serum cancer biomarkers positively correlated with the pathological progressions of COVID-19, demonstrating diffuse and acute lung injuries." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:0080600", "recommended_name": { "id": "DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, "synonyms": [ { "id": "DOID:0080600", "name": "SARS-CoV-2 infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan coronavirus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "COVID19", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan seafood market pneumonia virus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019-nCoV infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019 Novel Coronavirus (2019-nCoV)", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" } ] }, "evidence_source": [ { "id": "32347972", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32347972", "evidence_list": [ { "evidence": "This is the first report with such a substantial evaluation of cancer biomarkers on a large patient population of COVID-19. Our data demonstrate that levels of serum HE4, CYFRA21-1, CEA, CA125, CA153, SCC, and NSE are positively associated with CRP, a crucial factor in correlation with the severity of the disease. We concluded that elevations of serum cancer biomarkers positively correlated with the pathological progressions of COVID-19, demonstrating diffuse and acute pathophysiological injuries in COVID-19." }, { "evidence": "Increases in levels of Human epididymis protein 4 (HE4), Cytokeratin-19 fragment (CYFRA21-1) Carcinoembryonic antigen (CEA), Carbohydrate antigen 125 (CA125), Carbohydrate antigen 153 (CA153), Squamous cell carcinoma antigen (SCC), Carbohydrate antigen 199 (CA199). There were positive associations between levels of C-reactive protein and levels of HE4 (R= 0.631, p<0.001), CYFRA21-1 (R= 0.431, p<0.001), CEA (R= 0.316, p<0.001), SCC (R= 0.351, p<0.001), CA153 (R= 0.359, p<0.001) and CA125 (R= 0.223, p=0.031). We concluded that elevations of serum cancer biomarkers positively correlated with the pathological progressions of COVID-19, demonstrating diffuse and acute lung injuries." }, { "evidence": "Significant increases in levels of human epididymis protein 4 (HE4), cytokeratin-19 fragment (CYFRA21-1), carcinoembryonic antigen (CEA), carbohydrate antigens (CA) 125 , and 153 Squamous cell carcinoma antigen (SCC) and CA199 increased significantly." }, { "evidence": "Presence of elevated CYFRA21 levels shown as predictor of COVID-19 severity." } ], "tags": [ { "tag": "condition" }, { "tag": "best_biomarker_role" } ] }, { "id": "32504736", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32504736", "evidence_list": [ { "evidence": "In short, we concluded that the concentrations of tumor biomarkers of CEA, CYFRA21-1, NSE, SCCA, ProGRP were elevated in COVID-19 patients, and that CEA, CYFRA21-1, SCCA could predict the clinical outcome of COVID-19 patients." }, { "evidence": "Increased levels of CYFRA21-1 were observed in COVID-19 patients, and could predict the clinical outcome of patients." } ], "tags": [ { "tag": "condition" }, { "tag": "best_biomarker_role" } ] } ], "citation": [ { "title": "Elevations of serum cancer biomarkers correlate with severity of COVID-19.", "journal": "Journal of medical virology", "authors": "Wei X, Su J, Yang K, Wei J, Wan H, Cao X, Tan W, Wang H", "date": "2020-04-30", "evidence": [], "reference": [ { "id": "32347972", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32347972" } ] }, { "title": "Tumor biomarkers predict clinical outcome of COVID-19 patients.", "journal": "The Journal of infection", "authors": "He B, Zhong A, Wu Q, Liu X, Lin J, Chen C, He Y, Guo Y, Zhang M, Zhu P, Wu J, Wang C, Wang S, Xia X", "date": "2020-06-07", "evidence": [], "reference": [ { "id": "32504736", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32504736" } ] } ], "biomarker_canonical_id": "AN6315", "score": 1.2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 1 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6315-3", "biomarker_component": [ { "biomarker": "increased KRT19 level", "assessed_biomarker_entity": { "recommended_name": "Cytokeratin-19 fragment", "synonyms": [ { "synonym": "Cytokeratin-19" }, { "synonym": "CK-19" }, { "synonym": "Keratin-19" }, { "synonym": "K19" } ] }, "assessed_biomarker_entity_id": "UPKB:P08727", "assessed_entity_type": "protein", "specimen": [ { "name": "urine", "id": "UBERON:0001088", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0001088", "loinc_code": "" } ], "evidence_source": [ { "id": "25966163", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/25966163", "evidence_list": [ { "evidence": "In all studies considered, patients with bladder cancer had a higher CYFRA21-1 level than healthy subjects. Based on our results, CYFRA21-1 level may be a diagnostic biomarker for diagnosing bladder cancer as well as a possible biomarker for differentiation between local and metastatic bladder cancer." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0001088" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11054" }, "synonyms": [ { "id": "DOID:11054", "name": "tumor of the bladder", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11054" }, { "id": "DOID:11054", "name": "bladder cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11054" } ] }, "evidence_source": [ { "id": "25966163", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/25966163", "evidence_list": [ { "evidence": "In all studies considered, patients with bladder cancer had a higher CYFRA21-1 level than healthy subjects. Based on our results, CYFRA21-1 level may be a diagnostic biomarker for diagnosing bladder cancer as well as a possible biomarker for differentiation between local and metastatic bladder cancer." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "CYFRA21-1 levels could be a biomarker for bladder cancer: a meta-analysis.", "journal": "Genetics and molecular research : GMR", "authors": "Kuang LI, Song WJ, Qing HM, Yan S, Song FL", "date": "2015-05-13", "evidence": [], "reference": [ { "id": "25966163", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/25966163" } ] } ], "biomarker_canonical_id": "AN6315", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "c": "condition", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6316-1", "biomarker_component": [ { "biomarker": "decreased CEACAM5 level", "assessed_biomarker_entity": { "recommended_name": "Carcinoembryonic antigen", "synonyms": [ { "synonym": "Carcinoembryonic antigen" }, { "synonym": "CEA" }, { "synonym": "Meconium antigen 100" } ] }, "assessed_biomarker_entity_id": "UPKB:P06731", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "19166-8" } ], "evidence_source": [ { "id": "11953875", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/11953875", "evidence_list": [ { "evidence": "In those patients where marker levels of carcinoembryonic antigen decreased more than 33%, a significantly higher risk for relapse and death from disease (both P=0.0001) in univariate analyses was observed. In multivariate analysis this decrease of carcinoembryonic antigen proved to be an independent prognostic factor." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "name": "breast cancer", "description": "A thoracic cancer that originates in the mammary gland.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, "synonyms": [ { "id": "DOID:1612", "name": "malignant tumor of the breast", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "breast tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "mammary cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "primary breast cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "mammary tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "malignant neoplasm of breast", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" } ] }, "evidence_source": [ { "id": "11953875", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/11953875", "evidence_list": [ { "evidence": "In those patients where marker levels of carcinoembryonic antigen decreased more than 33%, a significantly higher risk for relapse and death from disease (both P=0.0001) in univariate analyses was observed. In multivariate analysis this decrease of carcinoembryonic antigen proved to be an independent prognostic factor." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Serum CEA and CA 15-3 as prognostic factors in primary breast cancer.", "journal": "British journal of cancer", "authors": "Ebeling FG, Stieber P, Untch M, Nagel D, Konecny GE, Schmitt UM, Fateh-Moghadam A, Seidel D", "date": "2002-04-16", "evidence": [], "reference": [ { "id": "11953875", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/11953875" } ] } ], "biomarker_canonical_id": "AN6316", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "c": "condition", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6320-2", "biomarker_component": [ { "biomarker": "increased CEACAM5 level", "assessed_biomarker_entity": { "recommended_name": "Carcinoembryonic antigen", "synonyms": [ { "synonym": "Carcinoembryonic antigen" }, { "synonym": "CEA" }, { "synonym": "Meconium antigen 100" } ] }, "assessed_biomarker_entity_id": "UPKB:P06731", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "19166-8" } ], "evidence_source": [ { "id": "12174919", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/12174919", "evidence_list": [ { "evidence": "In patients with colorectal cancer, CEA was most frequently elevated (54%), followed by CA 242 (46%), CA 19-9 (36%) and CA 72-4 (25%)." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_9256" }, "synonyms": [] }, "evidence_source": [ { "id": "12174919", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/12174919", "evidence_list": [ { "evidence": "In patients with colorectal cancer, CEA was most frequently elevated (54%), followed by CA 242 (46%), CA 19-9 (36%) and CA 72-4 (25%)." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "29168585", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/29168585", "evidence_list": [ { "evidence": "Elevated TBIL, DBIL, and CEA were significantly associated with poor 5-year OS in stage IV CRC patients. Moreover, DBIL could be considered as an independent prognostic biomarker for OS." } ], "tags": [ { "tag": "condition" }, { "tag": "best_biomarker_role" } ] } ], "citation": [ { "title": "CEA, CA 19-9 and CA 72-4 improve the diagnostic accuracy in gastrointestinal cancers.", "journal": "Anticancer research", "authors": "Carpelan-Holmström M, Louhimo J, Stenman UH, Alfthan H, Haglund C", "date": "2002-08-15", "evidence": [], "reference": [ { "id": "12174919", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/12174919" } ] }, { "title": "The prognostic impact of serum bilirubin in stage IV colorectal cancer patients.", "journal": "Journal of clinical laboratory analysis", "authors": "Yang L, Ge LY, Yu T, Liang Y, Yin Y, Chen H", "date": "2017-11-24", "evidence": [], "reference": [ { "id": "29168585", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/29168585" } ] } ], "biomarker_canonical_id": "AN6320", "score": 2.2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 1 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "w": "weight", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6318-1", "biomarker_component": [ { "biomarker": "Increase HE4 levels", "assessed_biomarker_entity": { "recommended_name": "Human epididymis protien 4", "synonyms": [ { "synonym": "Epididymal secretory protein E4" }, { "synonym": "Major epididymis-specific protein E4" }, { "synonym": "Putative protease inhibitor WAP5" } ] }, "assessed_biomarker_entity_id": "UPKB:Q14508", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "96044-3" } ], "evidence_source": [ { "id": "21683503", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/21683503", "evidence_list": [ { "evidence": "Our results demonstrated that an elevated serum HE4 level was related to the advanced stage of epithelial ovarian cancer. An elevated serum level of HE4 is a poor prognostic factor for PFS in patients with epithelial ovarian cancer who were treated with debulking surgery and adjuvant taxane and platinum-based chemotherapy." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:2394", "recommended_name": { "id": "DOID:2394", "name": "ovarian cancer", "description": "A female reproductive organ cancer that is located_in the ovary.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, "synonyms": [ { "id": "DOID:2394", "name": "primary ovarian cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "tumor of the Ovary", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "ovary neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "malignant tumour of ovary", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "malignant Ovarian tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "ovarian neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" } ] }, "evidence_source": [ { "id": "21683503", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/21683503", "evidence_list": [ { "evidence": "Our results demonstrated that an elevated serum HE4 level was related to the advanced stage of epithelial ovarian cancer. An elevated serum level of HE4 is a poor prognostic factor for PFS in patients with epithelial ovarian cancer who were treated with debulking surgery and adjuvant taxane and platinum-based chemotherapy." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Prognostic significance of human epididymis protein 4 in epithelial ovarian cancer.", "journal": "European journal of obstetrics, gynecology, and reproductive biology", "authors": "Paek J, Lee SH, Yim GW, Lee M, Kim YJ, Nam EJ, Kim SW, Kim YT", "date": "2011-06-21", "evidence": [], "reference": [ { "id": "21683503", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/21683503" } ] } ], "biomarker_canonical_id": "AN6318", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6746-1", "biomarker_component": [ { "biomarker": "increased CA125 levels", "assessed_biomarker_entity": { "recommended_name": "Cancer Antigen 125", "synonyms": [ { "synonym": "MUC-16" }, { "synonym": "Ovarian cancer-related tumor marker CA125" }, { "synonym": "CA-125" }, { "synonym": "Ovarian carcinoma antigen CA125" } ] }, "assessed_biomarker_entity_id": "UPKB:Q8WXI7", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "21683503", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/21683503", "evidence_list": [ { "evidence": "Our results demonstrated that an elevated serum HE4 level was related to the advanced stage of epithelial ovarian cancer. An elevated serum level of HE4 is a poor prognostic factor for PFS in patients with epithelial ovarian cancer who were treated with debulking surgery and adjuvant taxane and platinum-based chemotherapy." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:2394", "recommended_name": { "id": "DOID:2394", "name": "ovarian cancer", "description": "A female reproductive organ cancer that is located_in the ovary.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, "synonyms": [ { "id": "DOID:2394", "name": "primary ovarian cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "tumor of the Ovary", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "ovary neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "malignant tumour of ovary", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "malignant Ovarian tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "ovarian neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" } ] }, "evidence_source": [ { "id": "21683503", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/21683503", "evidence_list": [ { "evidence": "Our results demonstrated that an elevated serum HE4 level was related to the advanced stage of epithelial ovarian cancer. An elevated serum level of HE4 is a poor prognostic factor for PFS in patients with epithelial ovarian cancer who were treated with debulking surgery and adjuvant taxane and platinum-based chemotherapy." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32347972", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32347972", "evidence_list": [ { "evidence": "Additional cancer biomarkers such as carcinoembryonic antigen (CEA), carbohydrate antigens 125 and 153, squamous cell carcinoma antigen (SCC) and neuron-specific enolase (NSE) increased significantly in many critical cases. [DOI:10.2139/ssrn.3552854] Increases in levels of Human epididymis protein 4 (HE4), Cytokeratin-19 fragment (CYFRA21-1) Carcinoembryonic antigen (CEA), Carbohydrate antigen 125 (CA125), Carbohydrate antigen 153 (CA153), Squamous cell carcinoma antigen (SCC), Carbohydrate antigen 199 (CA199). There were positive associations between levels of C-reactive protein and levels of HE4 (R= 0.631, p<0.001), CYFRA21-1(R= 0.431, p<0.001), CEA (R= 0.316, p<0.001), SCC (R= 0.351, p<0.001), CA153 (R= 0.359, p<0.001) and CA125 (R= 0.223, p=0.031). We concluded that elevations of serum cancer biomarkers positively correlated with the pathological progressions of COVID-19, demonstrating diffuse and acute lung injuries." } ], "tags": [ { "tag": "condition" }, { "tag": "best_biomarker_role" } ] } ], "citation": [ { "title": "Prognostic significance of human epididymis protein 4 in epithelial ovarian cancer.", "journal": "European journal of obstetrics, gynecology, and reproductive biology", "authors": "Paek J, Lee SH, Yim GW, Lee M, Kim YJ, Nam EJ, Kim SW, Kim YT", "date": "2011-06-21", "evidence": [], "reference": [ { "id": "21683503", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/21683503" } ] }, { "title": "Elevations of serum cancer biomarkers correlate with severity of COVID-19.", "journal": "Journal of medical virology", "authors": "Wei X, Su J, Yang K, Wei J, Wan H, Cao X, Tan W, Wang H", "date": "2020-04-30", "evidence": [], "reference": [ { "id": "32347972", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32347972" } ] } ], "biomarker_canonical_id": "AN6746", "score": 1.2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 1 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "c": "condition", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6320-1", "biomarker_component": [ { "biomarker": "increased CEACAM5 level", "assessed_biomarker_entity": { "recommended_name": "Carcinoembryonic antigen", "synonyms": [ { "synonym": "Carcinoembryonic antigen" }, { "synonym": "CEA" }, { "synonym": "Meconium antigen 100" } ] }, "assessed_biomarker_entity_id": "UPKB:P06731", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "19166-8" } ], "evidence_source": [ { "id": "32347972", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32347972", "evidence_list": [ { "evidence": "Increases in levels of Human epididymis protein 4 (HE4), Cytokeratin-19 fragment (CYFRA21-1) Carcinoembryonic antigen (CEA), Carbohydrate antigen 125 (CA125), Carbohydrate antigen 153 (CA153), Squamous cell carcinoma antigen (SCC), Carbohydrate antigen 199 (CA199). There were positive associations between levels of C-reactive protein and levels of HE4 (R= 0.631, p<0.001), CYFRA21-1 (R= 0.431, p<0.001), CEA (R= 0.316, p<0.001), SCC (R= 0.351, p<0.001), CA153 (R= 0.359, p<0.001) and CA125 (R= 0.223, p=0.031). We concluded that elevations of serum cancer biomarkers positively correlated with the pathological progressions of COVID-19, demonstrating diffuse and acute lung injuries." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32333071", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32333071", "evidence_list": [ { "evidence": "On laboratory work-up, mildly elevated carcinoembryonic antigen (CEA = 9.8 ng/mL, normal range up to 5 ng/mL) was detected." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32540459", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32540459", "evidence_list": [ { "evidence": "In conclusion, the serum CEA levels were found to be increased in patients with severe or critically severe SARS-CoV-2 infection." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32504736", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32504736", "evidence_list": [ { "evidence": "In addition, the significant differences of plasma level of CEA, CYFRA21- 1 and SCCA were observed among the subgroups of severity of disease and clinical outcome (Table 1) and plasma level of CEA, CYFRA21-1, SCCA were significantly increased with the advance serverity of disease." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32504736", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32504736", "evidence_list": [ { "evidence": "Additional cancer biomarkers such as carcinoembryonic antigen (CEA), carbohydrate antigens 125 and 153, squamous cell carcinoma antigen (SCC) and neuron-specific enolase (NSE) increased significantly in many critical cases. [DOI:10.2139/ssrn.3552854] In addition, the significant differences of plasma level of CEA, CYFRA21- 1 and SCCA were observed among the subgroups of severity of disease and clinical outcome (Table 1) and plasma level of CEA, CYFRA21-1, SCCA were significantly increased with the advance serverity of disease." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32504736", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32504736", "evidence_list": [ { "evidence": "In short, we concluded that the concentrations of tumor biomarkers of CEA, CYFRA21-1, NSE, SCCA, ProGRP were elevated in COVID-19 patients, and that CEA, CYFRA21-1, SCCA could predict the clinical outcome of COVID-19 patients." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32347972", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32347972", "evidence_list": [ { "evidence": "Significant increases in levels of human epididymis protein 4 (HE4), cytokeratin-19 fragment (CYFRA21-1), carcinoembryonic antigen (CEA), carbohydrate antigens (CA) 125 , and 153 Squamous cell carcinoma antigen (SCC) and CA199 increased significantly." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32504736", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32504736", "evidence_list": [ { "evidence": "Tumor biomarkers, such as carcino embryonic antigen (CEA), cytokeratin 19 fragment (CYFRA21-1), neuron-specific enolase (NSE), squamous cell carcinoma antigen (SCCA) and Pro-Gastrin Releasing Peptide (ProGRP), were elevated." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32347972", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32347972", "evidence_list": [ { "evidence": "This is the first report with such a substantial evaluation of cancer biomarkers on a large patient population of COVID-19. Our data demonstrate that levels of serum HE4, CYFRA21-1, CEA, CA125, CA153, SCC, and NSE are positively associated with CRP, a crucial factor in correlation with the severity of the disease. We concluded that elevations of serum cancer biomarkers positively correlated with the pathological progressions of COVID-19, demonstrating diffuse and acute pathophysiological injuries in COVID-19." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "monitoring" } ], "condition": { "id": "DOID:0080600", "recommended_name": { "id": "DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, "synonyms": [ { "id": "DOID:0080600", "name": "SARS-CoV-2 infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan coronavirus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "COVID19", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan seafood market pneumonia virus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019-nCoV infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019 Novel Coronavirus (2019-nCoV)", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" } ] }, "evidence_source": [ { "id": "32333071", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32333071", "evidence_list": [ { "evidence": "On laboratory work-up, mildly elevated carcinoembryonic antigen (CEA = 9.8 ng/mL, normal range up to 5 ng/mL) was detected." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32540459", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32540459", "evidence_list": [ { "evidence": "In conclusion, the serum CEA levels were found to be increased in patients with severe or critically severe SARS-CoV-2 infection." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32347972", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32347972", "evidence_list": [ { "evidence": "Increases in levels of Human epididymis protein 4 (HE4), Cytokeratin-19 fragment (CYFRA21-1) Carcinoembryonic antigen (CEA), Carbohydrate antigen 125 (CA125), Carbohydrate antigen 153 (CA153), Squamous cell carcinoma antigen (SCC), Carbohydrate antigen 199 (CA199). There were positive associations between levels of C-reactive protein and levels of HE4 (R= 0.631, p<0.001), CYFRA21-1 (R= 0.431, p<0.001), CEA (R= 0.316, p<0.001), SCC (R= 0.351, p<0.001), CA153 (R= 0.359, p<0.001) and CA125 (R= 0.223, p=0.031). We concluded that elevations of serum cancer biomarkers positively correlated with the pathological progressions of COVID-19, demonstrating diffuse and acute lung injuries." }, { "evidence": "Significant increases in levels of human epididymis protein 4 (HE4), cytokeratin-19 fragment (CYFRA21-1), carcinoembryonic antigen (CEA), carbohydrate antigens (CA) 125 , and 153 Squamous cell carcinoma antigen (SCC) and CA199 increased significantly." }, { "evidence": "This is the first report with such a substantial evaluation of cancer biomarkers on a large patient population of COVID-19. Our data demonstrate that levels of serum HE4, CYFRA21-1, CEA, CA125, CA153, SCC, and NSE are positively associated with CRP, a crucial factor in correlation with the severity of the disease. We concluded that elevations of serum cancer biomarkers positively correlated with the pathological progressions of COVID-19, demonstrating diffuse and acute pathophysiological injuries in COVID-19." } ], "tags": [ { "tag": "condition" }, { "tag": "best_biomarker_role" } ] }, { "id": "32504736", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32504736", "evidence_list": [ { "evidence": "In addition, the significant differences of plasma level of CEA, CYFRA21- 1 and SCCA were observed among the subgroups of severity of disease and clinical outcome (Table 1) and plasma level of CEA, CYFRA21-1, SCCA were significantly increased with the advance serverity of disease." }, { "evidence": "Additional cancer biomarkers such as carcinoembryonic antigen (CEA), carbohydrate antigens 125 and 153, squamous cell carcinoma antigen (SCC) and neuron-specific enolase (NSE) increased significantly in many critical cases. [DOI:10.2139/ssrn.3552854] In addition, the significant differences of plasma level of CEA, CYFRA21- 1 and SCCA were observed among the subgroups of severity of disease and clinical outcome (Table 1) and plasma level of CEA, CYFRA21-1, SCCA were significantly increased with the advance serverity of disease." }, { "evidence": "In short, we concluded that the concentrations of tumor biomarkers of CEA, CYFRA21-1, NSE, SCCA, ProGRP were elevated in COVID-19 patients, and that CEA, CYFRA21-1, SCCA could predict the clinical outcome of COVID-19 patients." }, { "evidence": "Tumor biomarkers, such as carcino embryonic antigen (CEA), cytokeratin 19 fragment (CYFRA21-1), neuron-specific enolase (NSE), squamous cell carcinoma antigen (SCCA) and Pro-Gastrin Releasing Peptide (ProGRP), were elevated." } ], "tags": [ { "tag": "condition" }, { "tag": "best_biomarker_role" } ] } ], "citation": [ { "title": "Elevations of serum cancer biomarkers correlate with severity of COVID-19.", "journal": "Journal of medical virology", "authors": "Wei X, Su J, Yang K, Wei J, Wan H, Cao X, Tan W, Wang H", "date": "2020-04-30", "evidence": [], "reference": [ { "id": "32347972", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32347972" } ] }, { "title": "A case of COVID-19 lung infection first detected by [18F]FDG PET-CT.", "journal": "European journal of nuclear medicine and molecular imaging", "authors": "Amini H, Divband G, Montahaei Z, Dehghani T, Kaviani H, Adinehpour Z, Akbarian Aghdam R, Rezaee A, Vali R", "date": "2020-04-26", "evidence": [], "reference": [ { "id": "32333071", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32333071" } ] }, { "title": "Prognostic value of carcinoembryonic antigen on outcome in patients with coronavirus disease 2019.", "journal": "The Journal of infection", "authors": "Yu J, Yang Z, Zhou X, Wu D, Chen J, Zhang L, Tong L, Nie L", "date": "2020-06-17", "evidence": [], "reference": [ { "id": "32540459", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32540459" } ] }, { "title": "Tumor biomarkers predict clinical outcome of COVID-19 patients.", "journal": "The Journal of infection", "authors": "He B, Zhong A, Wu Q, Liu X, Lin J, Chen C, He Y, Guo Y, Zhang M, Zhu P, Wu J, Wang C, Wang S, Xia X", "date": "2020-06-07", "evidence": [], "reference": [ { "id": "32504736", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32504736" } ] } ], "biomarker_canonical_id": "AN6320", "score": 2.6, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 3 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "f": "frequency", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6411-2", "biomarker_component": [ { "biomarker": "increased PROGRP level", "assessed_biomarker_entity": { "recommended_name": "Progastrin releasing peptide", "synonyms": [] }, "assessed_biomarker_entity_id": "PRO:PR_000050383", "assessed_entity_type": "peptide", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "16033098", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/16033098", "evidence_list": [ { "evidence": "Tumor marker serum levels were related to histological type and tumor extension, CEA in adenocarcinomas. The most sensitive combinations of tumor markers were ProGRP and NSE in SCLC (88%), and CEA plus CYFRA in NSCLC (82%)." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "30994045", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30994045", "evidence_list": [ { "evidence": "Our results confirm that patients with lung cancer have increased serum levels of CEA, CYFRA 21-1, ProGRP, and NSE compared to patients with benign disease. Moreover, we found a strong association among the SCLC patients and high levels of ProGRP and NSE." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "16033098", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/16033098", "evidence_list": [ { "evidence": "Tumor marker serum levels were related to histological type and tumor extension, with ProGRP being the most sensitive marker in SCLC. The most sensitive combinations of tumor markers were ProGRP and NSE in SCLC (88%), and CEA plus CYFRA in NSCLC (82%). In summary, ProGRP is the tumor marker of choice in SCLC and NSE is a complementary tumor marker in this histological type." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32504736", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32504736", "evidence_list": [ { "evidence": "Tumor biomarkers, such as carcinoembryonic antigen (CEA), cytokeratin 19 fragment (CYFRA21-1), neuron-specific enolase (NSE), squamous cell carcinoma antigen (SCCA) and Pro-Gastrin Releasing Peptide (ProGRP), were elevated in cases than those in controls (pall<0.01." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "27747005", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/27747005", "evidence_list": [ { "evidence": "Plasma proGRP level could be a useful diagnostic and therapeutic monitoring biomarker for patients with SCLC and the initial level may help with SCLC tumor staging. At cutoff level of 63 pg/mL, proGRP shows 85.7% sensitivity, 90.2% specificity, 72.5% positive predictive value and 95.4% negative predictive value in patients with SCLC. Median proGRP level was higher in extensive disease (1,055.2 pg/mL) than limited disease (253.8 pg/mL, P=0.005). Median OS was significantly shorter in patients with extensive disease (6.0¬±0.7 months) than limited disease (12.7¬±4.5 months, P<0.01)." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "monitoring" } ], "condition": { "id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1324" }, "synonyms": [] }, "evidence_source": [ { "id": "16033098", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/16033098", "evidence_list": [ { "evidence": "Tumor marker serum levels were related to histological type and tumor extension, CEA in adenocarcinomas. The most sensitive combinations of tumor markers were ProGRP and NSE in SCLC (88%), and CEA plus CYFRA in NSCLC (82%)." }, { "evidence": "Tumor marker serum levels were related to histological type and tumor extension, with ProGRP being the most sensitive marker in SCLC. The most sensitive combinations of tumor markers were ProGRP and NSE in SCLC (88%), and CEA plus CYFRA in NSCLC (82%). In summary, ProGRP is the tumor marker of choice in SCLC and NSE is a complementary tumor marker in this histological type." } ], "tags": [ { "tag": "condition" }, { "tag": "best_biomarker_role" } ] }, { "id": "30994045", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30994045", "evidence_list": [ { "evidence": "Our results confirm that patients with lung cancer have increased serum levels of CEA, CYFRA 21-1, ProGRP, and NSE compared to patients with benign disease. Moreover, we found a strong association among the SCLC patients and high levels of ProGRP and NSE." } ], "tags": [ { "tag": "condition" }, { "tag": "best_biomarker_role" } ] }, { "id": "32504736", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32504736", "evidence_list": [ { "evidence": "Tumor biomarkers, such as carcinoembryonic antigen (CEA), cytokeratin 19 fragment (CYFRA21-1), neuron-specific enolase (NSE), squamous cell carcinoma antigen (SCCA) and Pro-Gastrin Releasing Peptide (ProGRP), were elevated in cases than those in controls (pall<0.01." } ], "tags": [ { "tag": "condition" }, { "tag": "best_biomarker_role" } ] }, { "id": "27747005", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/27747005", "evidence_list": [ { "evidence": "Plasma proGRP level could be a useful diagnostic and therapeutic monitoring biomarker for patients with SCLC and the initial level may help with SCLC tumor staging. At cutoff level of 63 pg/mL, proGRP shows 85.7% sensitivity, 90.2% specificity, 72.5% positive predictive value and 95.4% negative predictive value in patients with SCLC. Median proGRP level was higher in extensive disease (1,055.2 pg/mL) than limited disease (253.8 pg/mL, P=0.005). Median OS was significantly shorter in patients with extensive disease (6.0¬±0.7 months) than limited disease (12.7¬±4.5 months, P<0.01)." } ], "tags": [ { "tag": "condition" }, { "tag": "best_biomarker_role" } ] } ], "citation": [ { "title": "Pro-gastrin-releasing peptide (proGRP) in patients with benign and malignant diseases: comparison with CEA, SCC, CYFRA 21-1 and NSE in patients with lung cancer.", "journal": "Anticancer research", "authors": "Molina R, Auge JM, Filella X, Viñolas N, Alicarte J, Domingo JM, Ballesta AM", "date": "2005-07-22", "evidence": [], "reference": [ { "id": "16033098", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/16033098" } ] }, { "title": "New and old biomarkers in the differential diagnosis of lung cancer: Pro-gastrin-releasing peptide in comparison with neuron-specific enolase, carcinoembryonic antigen, and CYFRA 21-1.", "journal": "The International journal of biological markers", "authors": "Mauro C, Passerini R, Spaggiari L, Galetta D, Radice D, Lentati P, Sandri MT", "date": "2019-04-18", "evidence": [], "reference": [ { "id": "30994045", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30994045" } ] }, { "title": "Tumor biomarkers predict clinical outcome of COVID-19 patients.", "journal": "The Journal of infection", "authors": "He B, Zhong A, Wu Q, Liu X, Lin J, Chen C, He Y, Guo Y, Zhang M, Zhu P, Wu J, Wang C, Wang S, Xia X", "date": "2020-06-07", "evidence": [], "reference": [ { "id": "32504736", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32504736" } ] }, { "title": "Progastrin-releasing peptide as a diagnostic and therapeutic biomarker of small cell lung cancer.", "journal": "Journal of thoracic disease", "authors": "Oh HJ, Park HY, Kim KH, Park CK, Shin HJ, Lim JH, Kwon YS, Oh IJ, Kim YI, Lim SC, Kim YC, Kim SH, Shin MG", "date": "2016-10-18", "evidence": [], "reference": [ { "id": "27747005", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/27747005" } ] } ], "biomarker_canonical_id": "AN6411", "score": 1.6, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 3 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "c": "condition", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6322-1", "biomarker_component": [ { "biomarker": "increased MUC16 level", "assessed_biomarker_entity": { "recommended_name": "Mucin-16", "synonyms": [ { "synonym": "MUC-16" }, { "synonym": "Ovarian cancer-related tumor marker CA125" }, { "synonym": "CA-125" }, { "synonym": "Ovarian carcinoma antigen CA125" } ] }, "assessed_biomarker_entity_id": "UPKB:Q8WXI7", "assessed_entity_type": "protein", "specimen": [ { "name": "uterus", "id": "UBERON:0000995", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000995", "loinc_code": "10334-1" } ], "evidence_source": [ { "id": "29958235", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/29958235", "evidence_list": [ { "evidence": "The median levels of CA-125 were 9 to 14 times higher for each parameter that demonstrated extrauterine metastasis (all with P < 0.001). Levels of CA-125 were significantly associated with positive cytology (P < 0.0001), omental disease (P < 0.0001), pelvic or para-aortic lymph node metastasis (P < 0.0001), and adnexal involvement (P < 0.0001)." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000995" } ] } ] } ], "best_biomarker_role": [ { "role": "predictive" } ], "condition": { "id": "DOID:363", "recommended_name": { "id": "DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, "synonyms": [ { "id": "DOID:363", "name": "uterine tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "neoplasm of uterus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "Tumour of uterus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "malignant uterine tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "malignant neoplasm of uterus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "CA - cancer of uterus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "uterus neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" } ] }, "evidence_source": [ { "id": "29958235", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/29958235", "evidence_list": [ { "evidence": "The median levels of CA-125 were 9 to 14 times higher for each parameter that demonstrated extrauterine metastasis (all with P < 0.001). Levels of CA-125 were significantly associated with positive cytology (P < 0.0001), omental disease (P < 0.0001), pelvic or para-aortic lymph node metastasis (P < 0.0001), and adnexal involvement (P < 0.0001)." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Cancer Antigen 125 Levels are Significantly Associated With Prognostic Parameters in Uterine Papillary Serous Carcinoma.", "journal": "International journal of gynecological cancer : official journal of the International Gynecological Cancer Society", "authors": "Schmidt M, Segev Y, Sadeh R, Suzan E, Feferkorn I, Kaldawy A, Kligun G, Lavie O", "date": "2018-06-30", "evidence": [], "reference": [ { "id": "29958235", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/29958235" } ] } ], "biomarker_canonical_id": "AN6322", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "w": "weight", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6746-2", "biomarker_component": [ { "biomarker": "increased CA125 levels", "assessed_biomarker_entity": { "recommended_name": "Cancer Antigen 125", "synonyms": [ { "synonym": "MUC-16" }, { "synonym": "Ovarian cancer-related tumor marker CA125" }, { "synonym": "CA-125" }, { "synonym": "Ovarian carcinoma antigen CA125" } ] }, "assessed_biomarker_entity_id": "UPKB:Q8WXI7", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "24674678", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/24674678", "evidence_list": [ { "evidence": "The results indicate an increased level of CA15-3 in breast cancer patients (29.02+/-1.79 IU/ml) as compared to both women with benign tumor and healthy controls (13.78+/-1.24 and 8.92+/-0.48 IU/ml, respectively), and that this increase is associated to advanced stages. Patients with HER2/neu positive malignancies show elevated serum CA15-3 (37.09+/-2.55 IU/ml), as well as patients who developed recurrence (40.75+/-2.11 IU/ml). Study suggests that higher levels of CA 15-3 would be a reliable prognostic marker as they were directly related to advanced stages and recurrence. In addition, persistent elevation of CA 15-3 was associated to HER2/neu positivity in breast cancer patients." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "name": "breast cancer", "description": "A thoracic cancer that originates in the mammary gland.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, "synonyms": [ { "id": "DOID:1612", "name": "malignant tumor of the breast", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "breast tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "mammary cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "primary breast cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "mammary tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "malignant neoplasm of breast", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" } ] }, "evidence_source": [ { "id": "24674678", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/24674678", "evidence_list": [ { "evidence": "The results indicate an increased level of CA15-3 in breast cancer patients (29.02+/-1.79 IU/ml) as compared to both women with benign tumor and healthy controls (13.78+/-1.24 and 8.92+/-0.48 IU/ml, respectively), and that this increase is associated to advanced stages. Patients with HER2/neu positive malignancies show elevated serum CA15-3 (37.09+/-2.55 IU/ml), as well as patients who developed recurrence (40.75+/-2.11 IU/ml). Study suggests that higher levels of CA 15-3 would be a reliable prognostic marker as they were directly related to advanced stages and recurrence. In addition, persistent elevation of CA 15-3 was associated to HER2/neu positivity in breast cancer patients." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "The significance of CA15-3 in breast cancer patients and its relationship to HER-2 receptor status.", "journal": "International journal of immunopathology and pharmacology", "authors": "Hashim ZM", "date": "2014-03-29", "evidence": [], "reference": [ { "id": "24674678", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/24674678" } ] } ], "biomarker_canonical_id": "AN6746", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6324-1", "biomarker_component": [ { "biomarker": "increased MUC1 level", "assessed_biomarker_entity": { "recommended_name": "Mucin-1", "synonyms": [ { "synonym": "MUC-1" }, { "synonym": "Breast carcinoma-associated antigen DF3" }, { "synonym": "Cancer antigen 15-3" }, { "synonym": "CA 15-3" }, { "synonym": "Carcinoma-associated mucin" }, { "synonym": "Episialin" }, { "synonym": "H23AG" }, { "synonym": "Krebs von den Lungen-6" }, { "synonym": "KL-6" }, { "synonym": "PEMT" }, { "synonym": "Peanut-reactive urinary mucin" }, { "synonym": "PUM" }, { "synonym": "Polymorphic epithelial mucin" }, { "synonym": "PEM" }, { "synonym": "Tumor-associated epithelial membrane antigen" }, { "synonym": "EMA" }, { "synonym": "Tumor-associated mucin" } ] }, "assessed_biomarker_entity_id": "UPKB:P15941", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "19207-0" } ], "evidence_source": [ { "id": "24674678", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/24674678", "evidence_list": [ { "evidence": "The results indicate an increased level of CA15-3 in breast cancer patients (29.02+/-1.79 IU/ml) as compared to both women with benign tumor and healthy controls (13.78+/-1.24 and 8.92+/-0.48 IU/ml, respectively), and that this increase is associated to advanced stages. Patients with HER2/neu positive malignancies show elevated serum CA15-3 (37.09+/-2.55 IU/ml), as well as patients who developed recurrence (40.75+/-2.11 IU/ml). Study suggests that higher levels of CA 15-3 would be a reliable prognostic marker as they were directly related to advanced stages and recurrence. In addition, persistent elevation of CA 15-3 was associated to HER2/neu positivity in breast cancer patients." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "name": "breast cancer", "description": "A thoracic cancer that originates in the mammary gland.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, "synonyms": [ { "id": "DOID:1612", "name": "malignant tumor of the breast", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "breast tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "mammary cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "primary breast cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "mammary tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "malignant neoplasm of breast", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" } ] }, "evidence_source": [ { "id": "24674678", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/24674678", "evidence_list": [ { "evidence": "The results indicate an increased level of CA15-3 in breast cancer patients (29.02+/-1.79 IU/ml) as compared to both women with benign tumor and healthy controls (13.78+/-1.24 and 8.92+/-0.48 IU/ml, respectively), and that this increase is associated to advanced stages. Patients with HER2/neu positive malignancies show elevated serum CA15-3 (37.09+/-2.55 IU/ml), as well as patients who developed recurrence (40.75+/-2.11 IU/ml). Study suggests that higher levels of CA 15-3 would be a reliable prognostic marker as they were directly related to advanced stages and recurrence. In addition, persistent elevation of CA 15-3 was associated to HER2/neu positivity in breast cancer patients." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "The significance of CA15-3 in breast cancer patients and its relationship to HER-2 receptor status.", "journal": "International journal of immunopathology and pharmacology", "authors": "Hashim ZM", "date": "2014-03-29", "evidence": [], "reference": [ { "id": "24674678", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/24674678" } ] } ], "biomarker_canonical_id": "AN6324", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "f": "frequency", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6325-1", "biomarker_component": [ { "biomarker": "elevated KL-6 levels", "assessed_biomarker_entity": { "recommended_name": "Krebs von den Lungen-6", "synonyms": [ { "synonym": "MUC-1" }, { "synonym": "Breast carcinoma-associated antigen DF3" }, { "synonym": "Cancer antigen 15-3" }, { "synonym": "CA 15-3" }, { "synonym": "Carcinoma-associated mucin" }, { "synonym": "Episialin" }, { "synonym": "H23AG" }, { "synonym": "Krebs von den Lungen-6" }, { "synonym": "KL-6" }, { "synonym": "PEMT" }, { "synonym": "Peanut-reactive urinary mucin" }, { "synonym": "PUM" }, { "synonym": "Polymorphic epithelial mucin" }, { "synonym": "PEM" }, { "synonym": "Tumor-associated epithelial membrane antigen" }, { "synonym": "EMA" }, { "synonym": "Tumor-associated mucin" } ] }, "assessed_biomarker_entity_id": "UPKB:P15941", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": 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infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan coronavirus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "COVID19", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan seafood market pneumonia virus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019-nCoV infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019 Novel Coronavirus (2019-nCoV)", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" } ] }, "evidence_source": [ { "id": "32470148", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32470148", "evidence_list": [ { "evidence": "Increased KL-6 serum concentrations were observed in patients with severe pulmonary involvement, suggesting potential usefulness of KL-6 measurement to evaluate COVID-19 patients prognosis." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Serum KL-6 concentrations as a novel biomarker of severe COVID-19.", "journal": "Journal of medical virology", "authors": "d'Alessandro M, Cameli P, Refini RM, Bergantini L, Alonzi V, Lanzarone N, Bennett D, Rana GD, Montagnani F, Scolletta S, Franchi F, Frediani B, Valente S, Mazzei MA, Bonella F, Bargagli E", "date": "2020-05-30", "evidence": [], "reference": [ { "id": "32470148", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32470148" } ] } ], "biomarker_canonical_id": "AN6325", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "c": "condition", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6326-1", "biomarker_component": [ { "biomarker": "increased SART3 level", "assessed_biomarker_entity": { "recommended_name": "Squamous cell carcinoma antigen", "synonyms": [ { "synonym": "SART-3" }, { "synonym": "Tat-interacting protein of 110 kDa" }, { "synonym": "Tip110" }, { "synonym": "p110 nuclear RNA-binding protein" } ] }, "assessed_biomarker_entity_id": "UPKB:Q15020", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "19207-0" } ], "evidence_source": [ { "id": "32504736", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32504736", "evidence_list": [ { "evidence": "In addition, the significant differences of plasma level of CEA, CYFRA21- 1 and SCCA were observed among the subgroups of severity of disease and clinical outcome (Table 1) and plasma level of CEA, CYFRA21-1, SCCA were significantly increased with the advance serverity of disease." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32347972", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32347972", "evidence_list": [ { "evidence": "Additional cancer biomarkers such as carcinoembryonic antigen (CEA), carbohydrate antigens 125 and 153, squamous cell carcinoma antigen (SCC) and neuron-specific enolase (NSE) increased significantly in many critical cases. [DOI:10.2139/ssrn.3552854] Increases in levels of Human epididymis protein 4 (HE4), Cytokeratin-19 fragment (CYFRA21-1) Carcinoembryonic antigen (CEA), Carbohydrate antigen 125 (CA125), Carbohydrate antigen 153 (CA153), Squamous cell carcinoma antigen (SCC), Carbohydrate antigen 199 (CA199). There were positive associations between levels of C-reactive protein and levels of HE4 (R= 0.631, p<0.001), CYFRA21-1(R= 0.431, p<0.001), CEA (R= 0.316, p<0.001), SCC (R= 0.351, p<0.001), CA153 (R= 0.359, p<0.001) and CA125 (R= 0.223, p=0.031). We concluded that elevations of serum cancer biomarkers positively correlated with the pathological progressions of COVID-19, demonstrating diffuse and acute lung injuries." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32504736", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32504736", "evidence_list": [ { "evidence": "In short, we concluded that the concentrations of tumor biomarkers of CEA, CYFRA21-1, NSE, SCCA, ProGRP were elevated in COVID-19 patients, and that CEA, CYFRA21-1, SCCA could predict the clinical outcome of COVID-19 patients." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32347972", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32347972", "evidence_list": [ { "evidence": "Significant increases in levels of human epididymis protein 4 (HE4), cytokeratin-19 fragment (CYFRA21-1), carcinoembryonic antigen (CEA), carbohydrate antigens (CA) 125 , and 153 Squamous cell carcinoma antigen (SCC) and CA199 increased significantly." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32347972", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32347972", "evidence_list": [ { "evidence": "Presence of elevated CYFRA21 levels shown as predictor of COVID-19 severity:|Presence of elevated SCC levels shown as predictor of COVID-19 severity." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32504736", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32504736", "evidence_list": [ { "evidence": "Increased levels of CYFRA21-1 were observed in COVID-19 patients, and could predict the clinical outcome of patients." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32347972", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32347972", "evidence_list": [ { "evidence": "Squamous cell carcinoma antigen (SCC) and CA199 increased significantly only in critical cases of COVID-19 as compared with mild and severe cases and normal controls." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "monitoring" } ], "condition": { "id": "DOID:0080600", "recommended_name": { "id": "DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, "synonyms": [ { "id": "DOID:0080600", "name": "SARS-CoV-2 infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan coronavirus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "COVID19", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan seafood market pneumonia virus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019-nCoV infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019 Novel Coronavirus (2019-nCoV)", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" } ] }, "evidence_source": [ { "id": "32347972", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32347972", "evidence_list": [ { "evidence": "Additional cancer biomarkers such as carcinoembryonic antigen (CEA), carbohydrate antigens 125 and 153, squamous cell carcinoma antigen (SCC) and neuron-specific enolase (NSE) increased significantly in many critical cases. [DOI:10.2139/ssrn.3552854] Increases in levels of Human epididymis protein 4 (HE4), Cytokeratin-19 fragment (CYFRA21-1) Carcinoembryonic antigen (CEA), Carbohydrate antigen 125 (CA125), Carbohydrate antigen 153 (CA153), Squamous cell carcinoma antigen (SCC), Carbohydrate antigen 199 (CA199). There were positive associations between levels of C-reactive protein and levels of HE4 (R= 0.631, p<0.001), CYFRA21-1(R= 0.431, p<0.001), CEA (R= 0.316, p<0.001), SCC (R= 0.351, p<0.001), CA153 (R= 0.359, p<0.001) and CA125 (R= 0.223, p=0.031). We concluded that elevations of serum cancer biomarkers positively correlated with the pathological progressions of COVID-19, demonstrating diffuse and acute lung injuries." }, { "evidence": "Squamous cell carcinoma antigen (SCC) and CA199 increased significantly only in critical cases of COVID-19 as compared with mild and severe cases and normal controls." }, { "evidence": "Significant increases in levels of human epididymis protein 4 (HE4), cytokeratin-19 fragment (CYFRA21-1), carcinoembryonic antigen (CEA), carbohydrate antigens (CA) 125 , and 153 Squamous cell carcinoma antigen (SCC) and CA199 increased significantly." }, { "evidence": "Presence of elevated CYFRA21 levels shown as predictor of COVID-19 severity:|Presence of elevated SCC levels shown as predictor of COVID-19 severity." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32504736", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32504736", "evidence_list": [ { "evidence": "In addition, the significant differences of plasma level of CEA, CYFRA21- 1 and SCCA were observed among the subgroups of severity of disease and clinical outcome (Table 1) and plasma level of CEA, CYFRA21-1, SCCA were significantly increased with the advance serverity of disease." }, { "evidence": "In short, we concluded that the concentrations of tumor biomarkers of CEA, CYFRA21-1, NSE, SCCA, ProGRP were elevated in COVID-19 patients, and that CEA, CYFRA21-1, SCCA could predict the clinical outcome of COVID-19 patients." }, { "evidence": "Increased levels of CYFRA21-1 were observed in COVID-19 patients, and could predict the clinical outcome of patients." } ], "tags": [ { "tag": "condition" }, { "tag": "best_biomarker_role" } ] } ], "citation": [ { "title": "Tumor biomarkers predict clinical outcome of COVID-19 patients.", "journal": "The Journal of infection", "authors": "He B, Zhong A, Wu Q, Liu X, Lin J, Chen C, He Y, Guo Y, Zhang M, Zhu P, Wu J, Wang C, Wang S, Xia 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There were positive associations between levels of C-reactive protein and levels of HE4 (R= 0.631, p<0.001), CYFRA21-1(R= 0.431, p<0.001), CEA (R= 0.316, p<0.001), SCC (R= 0.351, p<0.001), CA153 (R= 0.359, p<0.001) and CA125 (R= 0.223, p=0.031). We concluded that elevations of serum cancer biomarkers positively correlated with the pathological progressions of COVID-19, demonstrating diffuse and acute lung injuries." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32347972", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32347972", "evidence_list": [ { "evidence": "Significant increases in levels of human epididymis protein 4 (HE4), cytokeratin-19 fragment (CYFRA21-1), carcinoembryonic antigen (CEA), carbohydrate antigens (CA) 125 , and 153. Squamous cell carcinoma antigen (SCC) and CA199 increased significantly." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "monitoring" } ], "condition": { "id": "DOID:0080600", "recommended_name": { "id": "DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, "synonyms": [ { "id": "DOID:0080600", "name": "SARS-CoV-2 infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan coronavirus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "COVID19", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan seafood market pneumonia virus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019-nCoV infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019 Novel Coronavirus (2019-nCoV)", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" } ] }, "evidence_source": [ { "id": "32347972", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32347972", "evidence_list": [ { "evidence": "Increases in levels of Human epididymis protein 4 (HE4), Cytokeratin-19 fragment (CYFRA21-1) Carcinoembryonic antigen (CEA), Carbohydrate antigen 125 (CA125), Carbohydrate antigen 153 (CA153), Squamous cell carcinoma antigen (SCC), Carbohydrate antigen 199 (CA199). There were positive associations between levels of C-reactive protein and levels of HE4 (R= 0.631, p<0.001), CYFRA21-1(R= 0.431, p<0.001), CEA (R= 0.316, p<0.001), SCC (R= 0.351, p<0.001), CA153 (R= 0.359, p<0.001) and CA125 (R= 0.223, p=0.031). We concluded that elevations of serum cancer biomarkers positively correlated with the pathological progressions of COVID-19, demonstrating diffuse and acute lung injuries." }, { "evidence": "Significant increases in levels of human epididymis protein 4 (HE4), cytokeratin-19 fragment (CYFRA21-1), carcinoembryonic antigen (CEA), carbohydrate antigens (CA) 125 , and 153. Squamous cell carcinoma antigen (SCC) and CA199 increased significantly." } ], "tags": [ { "tag": "condition" }, { "tag": "best_biomarker_role" } ] } ], "citation": [ { "title": "Elevations of serum cancer biomarkers correlate with severity of COVID-19.", "journal": "Journal of medical virology", "authors": "Wei X, Su J, Yang K, Wei J, Wan H, Cao X, Tan W, Wang H", "date": "2020-04-30", "evidence": [], "reference": [ { "id": "32347972", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32347972" } ] } ], "biomarker_canonical_id": "AN6328", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "w": "weight", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6329-1", "biomarker_component": [ { "biomarker": "increased CA199 level", "assessed_biomarker_entity": { "recommended_name": "Carbohydrate antigen 199", "synonyms": [] }, "assessed_biomarker_entity_id": "PCCID:643993", "assessed_entity_type": "glycan", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "32347972", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32347972", "evidence_list": [ { "evidence": "Squamous cell carcinoma antigen (SCC) and CA199 increased significantly only in critical cases of COVID-19 as compared with mild and severe cases and normal controls." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "risk" } ], "condition": { "id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "name": "COVID-19", "description": "A respiratory system cancer that is located_in the lung.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1324" }, "synonyms": [] }, "evidence_source": [], "citation": [ { "title": "Elevations of serum cancer biomarkers correlate with severity of COVID-19.", "journal": "Journal of medical virology", "authors": "Wei X, Su J, Yang K, Wei J, Wan H, Cao X, Tan W, Wang H", "date": "2020-04-30", "evidence": [], "reference": [ { "id": "32347972", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32347972" } ] } ], "biomarker_canonical_id": "AN6329", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6330-1", "biomarker_component": [ { "biomarker": "increased IFNG level", "assessed_biomarker_entity": { "recommended_name": "Interferon gamma", "synonyms": [ { "synonym": "IFN-gamma" }, { "synonym": "Immune interferon" } ] }, "assessed_biomarker_entity_id": "UPKB:P01579", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "12729-0" } ], "evidence_source": [ { "id": "31986264", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31986264", "evidence_list": [ { "evidence": "We noted that patients infected with 2019-nCoV also had high amounts of IL1B, IFN gamma, IP10, and MCP1, probably leading to activated T-helper-1 (Th1) cell responses. Initial plasma IL1B concentrations were higher in both ICU patients and non-ICU patients than in healthy adults." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32576222", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32576222", "evidence_list": [ { "evidence": "Levels of VEGF-D, TNF-alpha, SCF, LIF, IL-2, IL-4, IL-6, IL-8, IL-10, IL-15, IL-17A, IL-18, IL-1 beta, and IFN-gamma were significantly higher in the critical group than in the severe group (Table 1)." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "monitoring" } ], "condition": { "id": "DOID:0080600", "recommended_name": { "id": "DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, "synonyms": [ { "id": "DOID:0080600", "name": "SARS-CoV-2 infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan coronavirus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "COVID19", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan seafood market pneumonia virus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019-nCoV infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019 Novel Coronavirus (2019-nCoV)", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" } ] }, "evidence_source": [ { "id": "31986264", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31986264", "evidence_list": [ { "evidence": "We noted that patients infected with 2019-nCoV also had high amounts of IL1B, IFN gamma, IP10, and MCP1, probably leading to activated T-helper-1 (Th1) cell responses. Initial plasma IL1B concentrations were higher in both ICU patients and non-ICU patients than in healthy adults." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32576222", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32576222", "evidence_list": [ { "evidence": "Levels of VEGF-D, TNF-alpha, SCF, LIF, IL-2, IL-4, IL-6, IL-8, IL-10, IL-15, IL-17A, IL-18, IL-1 beta, and IFN-gamma were significantly higher in the critical group than in the severe group (Table 1)." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China.", "journal": "Lancet (London, England)", "authors": "Huang C, Wang Y, Li X, Ren L, Zhao J, Hu Y, Zhang L, Fan G, Xu J, Gu X, Cheng Z, Yu T, Xia J, Wei Y, Wu W, Xie X, Yin W, Li H, Liu M, Xiao Y, Gao H, Guo L, Xie J, Wang G, Jiang R, Gao Z, Jin Q, Wang J, Cao B", "date": "2020-01-28", "evidence": [], "reference": [ { "id": "31986264", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31986264" } ] }, { "title": "VEGF-D: a novel biomarker for detection of COVID-19 progression.", "journal": "Critical care (London, England)", "authors": "Kong Y, Han J, Wu X, Zeng H, Liu J, Zhang H", "date": "2020-06-25", "evidence": [], "reference": [ { "id": "32576222", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32576222" } ] } ], "biomarker_canonical_id": "AN6330", "score": 2.2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 1 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "f": "frequency", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6330-2", "biomarker_component": [ { "biomarker": "increased IFNG level", "assessed_biomarker_entity": { "recommended_name": "Interferon gamma", "synonyms": [ { "synonym": "IFN-gamma" }, { "synonym": "Immune interferon" } ] }, "assessed_biomarker_entity_id": "UPKB:P01579", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "12729-0" } ], "evidence_source": [ { "id": "15296648", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/15296648", "evidence_list": [ { "evidence": "IFN gamma level in patients from group 1 (T2DM) was 3.13 ¬± 0.92 pg/ml, group 2 (CC) 2.73 ¬± 0.91 pg/ ml, group 3 (T2DM and CC) 2.46 ¬± 0.98 pg/ml and group 4 (control) 5.02 ¬± 1.43 pg/ml; p < 0.05. There was no statistically significant difference in the concentration of IFN gamma in patients with T2DM and CC compared to other subjects. However, it has been demonstrated that level of IFN gamma in the control group and the group of patients with T2DM without CC was higher than in the other two groups." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:9351", "recommended_name": { "id": "DOID:9351", "name": "diabetes mellitus", "description": "A glucose metabolism disease that is characterized by chronic hyperglycaemia with disturbances of carbohydrate, fat and protein metabolism resulting from defects in insulin secretion, insulin action, or both.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_9351" }, "synonyms": [ { "id": "DOID:9351", "name": "diabetes", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_9351" } ] }, "evidence_source": [ { "id": "15296648", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/15296648", "evidence_list": [ { "evidence": "IFN gamma level in patients from group 1 (T2DM) was 3.13 ¬± 0.92 pg/ml, group 2 (CC) 2.73 ¬± 0.91 pg/ ml, group 3 (T2DM and CC) 2.46 ¬± 0.98 pg/ml and group 4 (control) 5.02 ¬± 1.43 pg/ml; p < 0.05. There was no statistically significant difference in the concentration of IFN gamma in patients with T2DM and CC compared to other subjects. However, it has been demonstrated that level of IFN gamma in the control group and the group of patients with T2DM without CC was higher than in the other two groups." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Intracellular IFN-gamma production and IL-12 serum levels in latent autoimmune diabetes of adults (LADA) and in type 2 diabetes.", "journal": "Journal of interferon & cytokine research : the official journal of the International Society for Interferon and Cytokine Research", "authors": "Tsiavou A, Degiannis D, Hatziagelaki E, Koniavitou K, Raptis SA", "date": "2004-08-07", "evidence": [], "reference": [ { "id": "15296648", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/15296648" } ] } ], "biomarker_canonical_id": "AN6330", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "w": "weight", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6331-1", "biomarker_component": [ { "biomarker": "increased CCL2 level", "assessed_biomarker_entity": { "recommended_name": "Monocyte chemoattractant protein 1", "synonyms": [ { "synonym": "HC11" }, { "synonym": "Monocyte chemoattractant protein 1" }, { "synonym": "Monocyte chemotactic and activating factor" }, { "synonym": "MCAF" }, { "synonym": "Monocyte chemotactic protein 1" }, { "synonym": "MCP-1" }, { "synonym": "Monocyte secretory protein JE" }, { "synonym": "Small-inducible cytokine A2" } ] }, "assessed_biomarker_entity_id": "UPKB:P13500", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "33303843", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/33303843", "evidence_list": [ { "evidence": "Elevated levels of pro-inflammatory cytokines were present in patients with severe COVID19. IL-6 and MCP-1 were inversely correlated with P/F with the largest AUC in ROC analyses and should be further explored as biomarkers to identify patients at risk for severe RF and as targets for improved treatment strategies." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "31986264", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31986264", "evidence_list": [ { "evidence": "We noted that patients infected with 2019-nCoV also had high amounts of IL1B, IFN gamma, IP10, and MCP1, probably leading to activated T-helper-1 (Th1) cell responses. Initial plasma IL1B concentrations were higher in both ICU patients and non-ICU patients than in healthy adults." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "monitoring" } ], "condition": { "id": "DOID:0080600", "recommended_name": { "id": "DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, "synonyms": [ { "id": "DOID:0080600", "name": "SARS-CoV-2 infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan coronavirus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "COVID19", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan seafood market pneumonia virus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019-nCoV infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019 Novel Coronavirus (2019-nCoV)", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" } ] }, "evidence_source": [ { "id": "33303843", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/33303843", "evidence_list": [ { "evidence": "Elevated levels of pro-inflammatory cytokines were present in patients with severe COVID19. IL-6 and MCP-1 were inversely correlated with P/F with the largest AUC in ROC analyses and should be further explored as biomarkers to identify patients at risk for severe RF and as targets for improved treatment strategies." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "31986264", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31986264", "evidence_list": [ { "evidence": "We noted that patients infected with 2019-nCoV also had high amounts of IL1B, IFN gamma, IP10, and MCP1, probably leading to activated T-helper-1 (Th1) cell responses. Initial plasma IL1B concentrations were higher in both ICU patients and non-ICU patients than in healthy adults." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Increased interleukin-6 and macrophage chemoattractant protein-1 are associated with respiratory failure in COVID-19.", "journal": "Scientific reports", "authors": "Jøntvedt Jørgensen M, Holter JC, Christensen EE, Schjalm C, Tonby K, Pischke SE, Jenum S, Skeie LG, Nur S, Lind A, Opsand H, Enersen TB, Grøndahl R, Hermann A, Dudman S, Muller F, Ueland T, Mollnes TE, Aukrust P, Heggelund L, Holten AR, Dyrhol-Riise AM", "date": "2020-12-12", "evidence": [], "reference": [ { "id": "33303843", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/33303843" } ] }, { "title": "Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China.", "journal": "Lancet (London, England)", "authors": "Huang C, Wang Y, Li X, Ren L, Zhao J, Hu Y, Zhang L, Fan G, Xu J, Gu X, Cheng Z, Yu T, Xia J, Wei Y, Wu W, Xie X, Yin W, Li H, Liu M, Xiao Y, Gao H, Guo L, Xie J, Wang G, Jiang R, Gao Z, Jin Q, Wang J, Cao B", "date": "2020-01-28", "evidence": [], "reference": [ { "id": "31986264", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31986264" } ] } ], "biomarker_canonical_id": "AN6331", "score": 1.2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 1 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "f": "frequency", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6331-2", "biomarker_component": [ { "biomarker": "increased CCL2 level", "assessed_biomarker_entity": { "recommended_name": "Monocyte chemoattractant protein 1", "synonyms": [ { "synonym": "HC11" }, { "synonym": "Monocyte chemoattractant protein 1" }, { "synonym": "Monocyte chemotactic and activating factor" }, { "synonym": "MCAF" }, { "synonym": "Monocyte chemotactic protein 1" }, { "synonym": "MCP-1" }, { "synonym": "Monocyte secretory protein JE" }, { "synonym": "Small-inducible cytokine A2" } ] }, "assessed_biomarker_entity_id": "UPKB:P13500", "assessed_entity_type": "protein", "specimen": [ { "name": "liver", "id": "UBERON:0002107", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0002107", "loinc_code": "" } ], "evidence_source": [ { "id": "19287949", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/19287949", "evidence_list": [ { "evidence": "Univariate analysis demonstrated that the timing of metastases, tumor size, number of metastases, and MCP-1 expression were significant prognostic factors. 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"assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "27161-9" }, { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "82334-4" } ], "evidence_source": [ { "id": "32222466", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32222466", "evidence_list": [ { "evidence": "2019-nCoV infection also initiated increased secretion of T-helper-2 (Th2) cytokines (eg, IL4 and IL10) that suppress inflammation, which differs from SARS-CoV infection." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32576222", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32576222", "evidence_list": [ { "evidence": "Levels of VEGF-D, TNF-alpha, SCF, LIF, IL-2, IL-4, IL-6, IL-8, IL-10, IL-15, IL-17A, IL-18, IL-1 beta, and IFN-gamma were significantly higher in the critical group than in the severe group (Table 1)." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "monitoring" } ], "condition": { "id": "DOID:0080600", "recommended_name": { "id": "DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, "synonyms": [ { "id": "DOID:0080600", "name": "SARS-CoV-2 infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan coronavirus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "COVID19", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan seafood market pneumonia virus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019-nCoV infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019 Novel Coronavirus (2019-nCoV)", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" } ] }, "evidence_source": [ { "id": "32222466", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32222466", "evidence_list": [ { "evidence": "2019-nCoV infection also initiated increased secretion of T-helper-2 (Th2) cytokines (eg, IL4 and IL10) that suppress inflammation, which differs from SARS-CoV infection." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32576222", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32576222", "evidence_list": [ { "evidence": "Levels of VEGF-D, TNF-alpha, SCF, LIF, IL-2, IL-4, IL-6, IL-8, IL-10, IL-15, IL-17A, IL-18, IL-1 beta, and IFN-gamma were significantly higher in the critical group than in the severe group (Table 1)." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "The use of anti-inflammatory drugs in the treatment of people with severe coronavirus disease 2019 (COVID-19): The Perspectives of clinical immunologists from China.", "journal": "Clinical immunology (Orlando, Fla.)", "authors": "Zhang W, Zhao Y, Zhang F, Wang Q, Li T, Liu Z, Wang J, Qin Y, Zhang X, Yan X, Zeng X, Zhang S", "date": "2020-03-31", "evidence": [], "reference": [ { "id": "32222466", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32222466" } ] }, { "title": "VEGF-D: a novel biomarker for detection of COVID-19 progression.", "journal": "Critical care (London, England)", "authors": "Kong Y, Han J, Wu X, Zeng H, Liu J, Zhang H", "date": "2020-06-25", "evidence": [], "reference": [ { "id": "32576222", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32576222" } ] } ], "biomarker_canonical_id": "AN6334", "score": 2.2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 1 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "c": "condition", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6334-2", "biomarker_component": [ { "biomarker": "increased IL4 level", "assessed_biomarker_entity": { "recommended_name": "Interleukin-4", "synonyms": [ { "synonym": "IL-4" }, { "synonym": "B-cell stimulatory factor 1" }, { "synonym": "BSF-1" }, { "synonym": "Binetrakin" }, { "synonym": "Lymphocyte stimulatory factor 1" }, { "synonym": "Pitrakinra" } ] }, "assessed_biomarker_entity_id": "UPKB:P05112", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "27161-9" } ], "evidence_source": [ { "id": "24213139", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/24213139", "evidence_list": [ { "evidence": "Serum IL-4 increased proportionately with disease progression. Our data are consistent with those reported in two smaller series both of which found that IL-4 levels increases as prostate cancer progresses to castrate resistant status." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "monitoring" } ], "condition": { "id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, "synonyms": [ { "id": "DOID:10283", "name": "prostate neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "NGP - new growth of prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "tumor of the prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostate cancer, familial", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostatic neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "malignant tumor of the prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "hereditary prostate cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostatic cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" } ] }, "evidence_source": [ { "id": "24213139", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/24213139", "evidence_list": [ { "evidence": "Serum IL-4 increased proportionately with disease progression. Our data are consistent with those reported in two smaller series both of which found that IL-4 levels increases as prostate cancer progresses to castrate resistant status." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Clinical investigation of the role of interleukin-4 and interleukin-13 in the evolution of prostate cancer.", "journal": "Cancers", "authors": "Goldstein R, Hanley C, Morris J, Cahill D, Chandra A, Harper P, Chowdhury S, Maher J, Burbridge S", "date": "2011-01-01", "evidence": [], "reference": [ { "id": "24213139", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/24213139" } ] } ], "biomarker_canonical_id": "AN6334", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "c": "condition", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6278-6", "biomarker_component": [ { "biomarker": "increased IL6 level", "assessed_biomarker_entity": { "recommended_name": "Interleukin-6", "synonyms": [ { "synonym": "IL-6" }, { "synonym": "B-cell stimulatory factor 2" }, { "synonym": "BSF-2" }, { "synonym": "CTL differentiation factor" }, { "synonym": "CDF" }, { "synonym": "Hybridoma growth factor" }, { "synonym": "Interferon beta-2" }, { "synonym": "IFN-beta-2" } ] }, "assessed_biomarker_entity_id": "UPKB:P05231", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "26848-2" } ], "evidence_source": [ { "id": "30304975", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30304975", "evidence_list": [ { "evidence": "IL-6, IL-8, and IL-10 showed significant positive correlations with each other. Moreover, high levels of serum IL-6, IL-8, and IL-10 were independently strongly associated with poor survival of patients with pancreatic cancer. Patients with high IL-6, IL-8, or IL-10 expression (greater than median expression levels) exhibited a significantly shorter survival time, compared with patients with low expression (less than median expression levels) (p<0.001 for IL-6, p<0.01 for IL-8, and p<0.05 for IL-10) Univariate Cox analysis revealed that a high expression level of either IL-6, IL-8, or IL-10 was associated with poor survival (IL-6: HR = 0.204, 95% CI: 0.107-0.410, p<0.001; IL-8: HR = 0.303, 95% CI: 0.135-0.683, p<0.01; IL-10: HR = 0.336, 95% CI: 0.125-0.900, p<0.05)." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:1793", "recommended_name": { "id": "DOID:1793", "name": "pancreatic cancer", "description": "An endocrine gland cancer located_in the pancreas.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, "synonyms": [ { "id": "DOID:1793", "name": "Ca head of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "Ca body of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "pancreatic tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "malignant neoplasm of tail of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "malignant neoplasm of head of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "pancreatic neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "Ca tail of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "pancreas neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "malignant neoplasm of body of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" } ] }, "evidence_source": [ { "id": "30304975", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30304975", "evidence_list": [ { "evidence": "IL-6, IL-8, and IL-10 showed significant positive correlations with each other. Moreover, high levels of serum IL-6, IL-8, and IL-10 were independently strongly associated with poor survival of patients with pancreatic cancer. Patients with high IL-6, IL-8, or IL-10 expression (greater than median expression levels) exhibited a significantly shorter survival time, compared with patients with low expression (less than median expression levels) (p<0.001 for IL-6, p<0.01 for IL-8, and p<0.05 for IL-10) Univariate Cox analysis revealed that a high expression level of either IL-6, IL-8, or IL-10 was associated with poor survival (IL-6: HR = 0.204, 95% CI: 0.107-0.410, p<0.001; IL-8: HR = 0.303, 95% CI: 0.135-0.683, p<0.01; IL-10: HR = 0.336, 95% CI: 0.125-0.900, p<0.05)." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Serum levels of IL-6, IL-8, and IL-10 are indicators of prognosis in pancreatic cancer.", "journal": "The Journal of international medical research", "authors": "Feng L, Qi Q, Wang P, Chen H, Chen Z, Meng Z, Liu L", "date": "2018-10-12", "evidence": [], "reference": [ { "id": "30304975", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30304975" } ] } ], "biomarker_canonical_id": "AN6278", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "f": "frequency", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6372-4", "biomarker_component": [ { "biomarker": "increased IL8 level", "assessed_biomarker_entity": { "recommended_name": "Interleukin-8", "synonyms": [ { "synonym": "IL-8" }, { "synonym": "C-X-C motif chemokine 8" }, { "synonym": "Chemokine (C-X-C motif) ligand 8" }, { "synonym": "Emoctakin" }, { "synonym": "Granulocyte chemotactic protein 1" }, { "synonym": "GCP-1" }, { "synonym": "Monocyte-derived neutrophil chemotactic factor" }, { "synonym": "MDNCF" }, { "synonym": "Monocyte-derived neutrophil-activating peptide" }, { "synonym": "MONAP" }, { "synonym": "Neutrophil-activating protein 1" }, { "synonym": "NAP-1" }, { "synonym": "Protein 3-10C" }, { "synonym": "T-cell chemotactic factor" } ] }, "assessed_biomarker_entity_id": "UPKB:P10145", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "33211-4" } ], "evidence_source": [ { "id": "30304975", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30304975", "evidence_list": [ { "evidence": "IL-6, IL-8, and IL-10 showed significant positive correlations with each other. Moreover, high levels of serum IL-6, IL-8, and IL-10 were independently strongly associated with poor survival of patients with pancreatic cancer. Patients with high IL-6, IL-8, or IL-10 expression (greater than median expression levels) exhibited a significantly shorter survival time, compared with patients with low expression (less than median expression levels) (p<0.001 for IL-6, p<0.01 for IL-8, and p<0.05 for IL-10) Univariate Cox analysis revealed that a high expression level of either IL-6, IL-8, or IL-10 was associated with poor survival (IL-6: HR = 0.204, 95% CI: 0.107-0.410, p<0.001; IL-8: HR = 0.303, 95% CI: 0.135-0.683, p<0.01; IL-10: HR = 0.336, 95% CI: 0.125-0.900, p<0.05)." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:1793", "recommended_name": { "id": "DOID:1793", "name": "pancreatic cancer", "description": "An endocrine gland cancer located_in the pancreas.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, "synonyms": [ { "id": "DOID:1793", "name": "Ca head of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "Ca body of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "pancreatic tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "malignant neoplasm of tail of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "malignant neoplasm of head of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "pancreatic neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "Ca tail of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "pancreas neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "malignant neoplasm of body of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" } ] }, "evidence_source": [ { "id": "30304975", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30304975", "evidence_list": [ { "evidence": "IL-6, IL-8, and IL-10 showed significant positive correlations with each other. Moreover, high levels of serum IL-6, IL-8, and IL-10 were independently strongly associated with poor survival of patients with pancreatic cancer. Patients with high IL-6, IL-8, or IL-10 expression (greater than median expression levels) exhibited a significantly shorter survival time, compared with patients with low expression (less than median expression levels) (p<0.001 for IL-6, p<0.01 for IL-8, and p<0.05 for IL-10) Univariate Cox analysis revealed that a high expression level of either IL-6, IL-8, or IL-10 was associated with poor survival (IL-6: HR = 0.204, 95% CI: 0.107-0.410, p<0.001; IL-8: HR = 0.303, 95% CI: 0.135-0.683, p<0.01; IL-10: HR = 0.336, 95% CI: 0.125-0.900, p<0.05)." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Serum levels of IL-6, IL-8, and IL-10 are indicators of prognosis in pancreatic cancer.", "journal": "The Journal of international medical research", "authors": "Feng L, Qi Q, Wang P, Chen H, Chen Z, Meng Z, Liu L", "date": "2018-10-12", "evidence": [], "reference": [ { "id": "30304975", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30304975" } ] } ], "biomarker_canonical_id": "AN6372", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6337-1", "biomarker_component": [ { "biomarker": "increased IL10 level", "assessed_biomarker_entity": { "recommended_name": "Interleukin-10", "synonyms": [ { "synonym": "IL-10" }, { "synonym": "Cytokine synthesis inhibitory factor" }, { "synonym": "CSIF" } ] }, "assessed_biomarker_entity_id": "UPKB:P22301", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "26848-2" } ], "evidence_source": [ { "id": "30304975", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30304975", "evidence_list": [ { "evidence": "IL-6, IL-8, and IL-10 showed significant positive correlations with each other. Moreover, high levels of serum IL-6, IL-8, and IL-10 were independently strongly associated with poor survival of patients with pancreatic cancer. Patients with high IL-6, IL-8, or IL-10 expression (greater than median expression levels) exhibited a significantly shorter survival time, compared with patients with low expression (less than median expression levels) (p<0.001 for IL-6, p<0.01 for IL-8, and p<0.05 for IL-10) Univariate Cox analysis revealed that a high expression level of either IL-6, IL-8, or IL-10 was associated with poor survival (IL-6: HR = 0.204, 95% CI: 0.107-0.410, p<0.001; IL-8: HR = 0.303, 95% CI: 0.135-0.683, p<0.01; IL-10: HR = 0.336, 95% CI: 0.125-0.900, p<0.05)." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:1793", "recommended_name": { "id": "DOID:1793", "name": "pancreatic cancer", "description": "An endocrine gland cancer located_in the pancreas.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, "synonyms": [ { "id": "DOID:1793", "name": "Ca head of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "Ca body of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "pancreatic tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "malignant neoplasm of tail of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "malignant neoplasm of head of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "pancreatic neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "Ca tail of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "pancreas neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "malignant neoplasm of body of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" } ] }, "evidence_source": [ { "id": "30304975", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30304975", "evidence_list": [ { "evidence": "IL-6, IL-8, and IL-10 showed significant positive correlations with each other. Moreover, high levels of serum IL-6, IL-8, and IL-10 were independently strongly associated with poor survival of patients with pancreatic cancer. Patients with high IL-6, IL-8, or IL-10 expression (greater than median expression levels) exhibited a significantly shorter survival time, compared with patients with low expression (less than median expression levels) (p<0.001 for IL-6, p<0.01 for IL-8, and p<0.05 for IL-10) Univariate Cox analysis revealed that a high expression level of either IL-6, IL-8, or IL-10 was associated with poor survival (IL-6: HR = 0.204, 95% CI: 0.107-0.410, p<0.001; IL-8: HR = 0.303, 95% CI: 0.135-0.683, p<0.01; IL-10: HR = 0.336, 95% CI: 0.125-0.900, p<0.05)." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Serum levels of IL-6, IL-8, and IL-10 are indicators of prognosis in pancreatic cancer.", "journal": "The Journal of international medical research", "authors": "Feng L, Qi Q, Wang P, Chen H, Chen Z, Meng Z, Liu L", "date": "2018-10-12", "evidence": [], "reference": [ { "id": "30304975", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30304975" } ] } ], "biomarker_canonical_id": "AN6337", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6337-2", "biomarker_component": [ { "biomarker": "increased IL10 level", "assessed_biomarker_entity": { "recommended_name": "Interleukin-10", "synonyms": [ { "synonym": "IL-10" }, { "synonym": "Cytokine synthesis inhibitory factor" }, { "synonym": "CSIF" } ] }, "assessed_biomarker_entity_id": "UPKB:P22301", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "26848-2" } ], "evidence_source": [ { "id": "31986264", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31986264", "evidence_list": [ { "evidence": "Comparison between ICU and non-ICU patients showed that plasma concentrations of IL2, IL7, IL10, GCSF, IP10, MCP1, MIP1A, and TNF alpha were higher in ICU patients than non-ICU patients. Compared with non-ICU patients, ICU patients had higher plasma levels of IL2, IL7, IL10, GSCF, IP10, MCP1, MIP1A, and TNF alpha." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32222466", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32222466", "evidence_list": [ { "evidence": "IL-2, IL-7, IL-10, G-CSF, IP10, MCP1, MIP1A, TNF alpha were higher in severe patients." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "33349241", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/33349241", "evidence_list": [ { "evidence": "Significant correlations were found about age, IL2R, IL-6, IL-8, IL-10, TNFα, CRP, ferroprotein, PCT, LC, NC, and EC. PCT (R = -0.650), CRP (R = -0.604), NC (R = -0.585), age (R = -0.564), LC (R = 0.56), IL-6 (R = -0.535), IL2R (R = -0.534) and ferroprotein (R = -0.508) were highly correlated." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32576222", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32576222", "evidence_list": [ { "evidence": "Levels of VEGF-D, TNF-alpha, SCF, LIF, IL-2, IL-4, IL-6, IL-8, IL-10, IL-15, IL-17A, IL-18, IL-1 beta, and IFN-gamma were significantly higher in the critical group than in the severe group (Table 1)." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "monitoring" } ], "condition": { "id": "DOID:0080600", "recommended_name": { "id": "DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, "synonyms": [ { "id": "DOID:0080600", "name": "SARS-CoV-2 infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan coronavirus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "COVID19", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan seafood market pneumonia virus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019-nCoV infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019 Novel Coronavirus (2019-nCoV)", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" } ] }, "evidence_source": [ { "id": "31986264", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31986264", "evidence_list": [ { "evidence": "Comparison between ICU and non-ICU patients showed that plasma concentrations of IL2, IL7, IL10, GCSF, IP10, MCP1, MIP1A, and TNF alpha were higher in ICU patients than non-ICU patients. Compared with non-ICU patients, ICU patients had higher plasma levels of IL2, IL7, IL10, GSCF, IP10, MCP1, MIP1A, and TNF alpha." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32222466", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32222466", "evidence_list": [ { "evidence": "IL-2, IL-7, IL-10, G-CSF, IP10, MCP1, MIP1A, TNF alpha were higher in severe patients." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "33349241", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/33349241", "evidence_list": [ { "evidence": "Significant correlations were found about age, IL2R, IL-6, IL-8, IL-10, TNFα, CRP, ferroprotein, PCT, LC, NC, and EC. PCT (R = -0.650), CRP (R = -0.604), NC (R = -0.585), age (R = -0.564), LC (R = 0.56), IL-6 (R = -0.535), IL2R (R = -0.534) and ferroprotein (R = -0.508) were highly correlated." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32576222", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32576222", "evidence_list": [ { "evidence": "Levels of VEGF-D, TNF-alpha, SCF, LIF, IL-2, IL-4, IL-6, IL-8, IL-10, IL-15, IL-17A, IL-18, IL-1 beta, and IFN-gamma were significantly higher in the critical group than in the severe group (Table 1)." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China.", "journal": "Lancet (London, England)", "authors": "Huang C, Wang Y, Li X, Ren L, Zhao J, Hu Y, Zhang L, Fan G, Xu J, Gu X, Cheng Z, Yu T, Xia J, Wei Y, Wu W, Xie X, Yin W, Li H, Liu M, Xiao Y, Gao H, Guo L, Xie J, Wang G, Jiang R, Gao Z, Jin Q, Wang J, Cao B", "date": "2020-01-28", "evidence": [], "reference": [ { "id": "31986264", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31986264" } ] }, { "title": "The use of anti-inflammatory drugs in the treatment of people with severe coronavirus disease 2019 (COVID-19): The Perspectives of clinical immunologists from China.", "journal": "Clinical immunology (Orlando, Fla.)", "authors": "Zhang W, Zhao Y, Zhang F, Wang Q, Li T, Liu Z, Wang J, Qin Y, Zhang X, Yan X, Zeng X, Zhang S", "date": "2020-03-31", "evidence": [], "reference": [ { "id": "32222466", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32222466" } ] }, { "title": "Correlation analysis between disease severity and inflammation-related parameters in patients with COVID-19: a retrospective study.", "journal": "BMC infectious diseases", "authors": "Gong J, Dong H, Xia QS, Huang ZY, Wang DK, Zhao Y, Liu WH, Tu SH, Zhang MM, Wang Q, Lu FE", "date": "2020-12-23", "evidence": [], "reference": [ { "id": "33349241", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/33349241" } ] }, { "title": "VEGF-D: a novel biomarker for detection of COVID-19 progression.", "journal": "Critical care (London, England)", "authors": "Kong Y, Han J, Wu X, Zeng H, Liu J, Zhang H", "date": "2020-06-25", "evidence": [], "reference": [ { "id": "32576222", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32576222" } ] } ], "biomarker_canonical_id": "AN6337", "score": 2.6, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 3 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "f": "frequency", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6338-1", "biomarker_component": [ { "biomarker": "decreased IL10 level", "assessed_biomarker_entity": { "recommended_name": "Interleukin-10", "synonyms": [ { "synonym": "IL-10" }, { "synonym": "Cytokine synthesis inhibitory factor" }, { "synonym": "CSIF" } ] }, "assessed_biomarker_entity_id": "UPKB:P22301", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "26848-2" } ], "evidence_source": [ { "id": "28420440", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/28420440", "evidence_list": [ { "evidence": "A reduction of plasma interleukin-10 levels significantly correlated with an increase in the mean number of metabolic risk factors such as increased waist circumference, BMI, dyslipidaemia, high blood pressure and glucose intolerance." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "predictive" } ], "condition": { "id": "DOID:9351", "recommended_name": { "id": "DOID:9351", "name": "diabetes mellitus", "description": "A glucose metabolism disease that is characterized by chronic hyperglycaemia with disturbances of carbohydrate, fat and protein metabolism resulting from defects in insulin secretion, insulin action, or both.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_9351" }, "synonyms": [ { "id": "DOID:9351", "name": "diabetes", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_9351" } ] }, "evidence_source": [ { "id": "28420440", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/28420440", "evidence_list": [ { "evidence": "A reduction of plasma interleukin-10 levels significantly correlated with an increase in the mean number of metabolic risk factors such as increased waist circumference, BMI, dyslipidaemia, high blood pressure and glucose intolerance." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Immune response after autologous hematopoietic stem cell transplantation in type 1 diabetes mellitus.", "journal": "Stem cell research & therapy", "authors": "Ye L, Li L, Wan B, Yang M, Hong J, Gu W, Wang W, Ning G", "date": "2017-04-20", "evidence": [], "reference": [ { "id": "28420440", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/28420440" } ] } ], "biomarker_canonical_id": "AN6338", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "w": "weight", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6339-1", "biomarker_component": [ { "biomarker": "increased CREA level", "assessed_biomarker_entity": { "recommended_name": "Creatinine", "synonyms": [ { "synonym": "1-Methylglycocyamidine" }, { "synonym": "creatinine" }, { "synonym": "Creatinine" }, { "synonym": "2-amino-1,5-dihydro-1-methyl-4H-Imidazol-4-one" }, { "synonym": "Kreatinin" }, { "synonym": "1-methylglycocyamidine" }, { "synonym": "1-Methylhydantoin-2-imide" }, { "synonym": "creatinina" }, { "synonym": "2-imino-1-methylimidazolidin-4-one" }, { "synonym": "2-Amino-1-methylimidazolin-4-one" }, { "synonym": "Creatine anhydride" } ] }, "assessed_biomarker_entity_id": "CHEBI:16737", "assessed_entity_type": "metabolite", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "38483-4" } ], "evidence_source": [ { "id": "32475810", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32475810", "evidence_list": [ { "evidence": "A larger study of 701 patients revealed that elevated serum creatinine levels on admission correlated with severity due to significant abnormalities in the coagulation pathway." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32247631", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32247631", "evidence_list": [ { "evidence": "We found that patients with elevated baseline serum creatinine were more likely to be admitted to the intensive care unit and to undergo mechanical ventilation." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "monitoring" } ], "condition": { "id": "DOID:0080600", "recommended_name": { "id": "DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, "synonyms": [ { "id": "DOID:0080600", "name": "SARS-CoV-2 infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan coronavirus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "COVID19", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan seafood market pneumonia virus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019-nCoV infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019 Novel Coronavirus (2019-nCoV)", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" } ] }, "evidence_source": [ { "id": "32475810", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32475810", "evidence_list": [ { "evidence": "A larger study of 701 patients revealed that elevated serum creatinine levels on admission correlated with severity due to significant abnormalities in the coagulation pathway." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32247631", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32247631", "evidence_list": [ { "evidence": "We found that patients with elevated baseline serum creatinine were more likely to be admitted to the intensive care unit and to undergo mechanical ventilation." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "The role of biomarkers in diagnosis of COVID-19 - A systematic review.", "journal": "Life sciences", "authors": "Kermali M, Khalsa RK, Pillai K, Ismail Z, Harky A", "date": "2020-06-02", "evidence": [], "reference": [ { "id": "32475810", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32475810" } ] }, { "title": "Kidney disease is associated with in-hospital death of patients with COVID-19.", "journal": "Kidney international", "authors": "Cheng Y, Luo R, Wang K, Zhang M, Wang Z, Dong L, Li J, Yao Y, Ge S, Xu G", "date": "2020-04-06", "evidence": [], "reference": [ { "id": "32247631", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32247631" } ] } ], "biomarker_canonical_id": "AN6339", "score": 2.2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 1 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "c": "condition", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6340-1", "biomarker_component": [ { "biomarker": "Increased BUN level", 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Among all, lymphopenia, thrombocytopenia, leucocytosis, CRP, PCT, LDH, AST, ALT, D-dimer, cTn represent the most predictive parameters of severe COVID-19" } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] }, { "biomarker": "increased PCT level", "assessed_biomarker_entity": { "recommended_name": "Procalcitonin", "synonyms": [] }, "assessed_biomarker_entity_id": "UPKB:P01258", "assessed_entity_type": "protein complex", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "32766546", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32766546", "evidence_list": [ { "evidence": "On multivariable analysis, the risk factors found to be significantly associated with admission to intensive care were age above 50 years old, a qSOFA score above 0, smoking, elevated CRP and elevated procalcitonin levels. Asthma, smoking and elevated procalcitonin levels correlated significantly with mortality in our cohort." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "monitoring" } ], "condition": { "id": "DOID:0080600", "recommended_name": { "id": "DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, "synonyms": [ { "id": "DOID:0080600", "name": "SARS-CoV-2 infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan coronavirus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "COVID19", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan seafood market pneumonia virus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019-nCoV infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019 Novel Coronavirus (2019-nCoV)", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" } ] }, "evidence_source": [ { "id": "32505227", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32505227", "evidence_list": [ { "evidence": "Other consistently reported markers in non-survivors are increased procalcitonin (PCT) and IL-6 levels, as well as increased serum urea, creatinine, cystatin C, direct bilirubin, and cholinesterase." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32589600", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32589600", "evidence_list": [ { "evidence": "Many biomarkers have been associated with poor outcomes and represent a candidate for risk stratification models for predicting severe COVID-19 in order to guide clinical care. Among all, lymphopenia, thrombocytopenia, leucocytosis, CRP, PCT, LDH, AST, ALT, D-dimer, cTn represent the most predictive parameters of severe COVID-19" } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32766546", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32766546", "evidence_list": [ { "evidence": "On multivariable analysis, the risk factors found to be significantly associated with admission to intensive care were age above 50 years old, a qSOFA score above 0, smoking, elevated CRP and elevated procalcitonin levels. Asthma, smoking and elevated procalcitonin levels correlated significantly with mortality in our cohort." } ], "tags": [ { "tag": "condition" }, { "tag": "best_biomarker_role" } ] } ], "citation": [ { "title": "Immunology of COVID-19: Current State of the Science.", "journal": "Immunity", "authors": "Vabret N, Britton GJ, Gruber C, Hegde S, Kim J, Kuksin M, Levantovsky R, Malle L, Moreira A, Park MD, Pia L, Risson E, Saffern M, Salomé B, Esai Selvan M, Spindler MP, Tan J, van der Heide V, Gregory JK, Alexandropoulos K, Bhardwaj N, Brown BD, Greenbaum B, Gümüş ZH, Homann D, Horowitz A, Kamphorst AO, Curotto de Lafaille MA, Mehandru S, Merad M, Samstein RM, None None", "date": "2020-06-09", "evidence": [], "reference": [ { "id": "32505227", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32505227" } ] }, { "title": "Biochemical biomarkers alterations in Coronavirus Disease 2019 (COVID-19).", "journal": "Diagnosis (Berlin, Germany)", "authors": "Ciaccio M, Agnello L", "date": "2020-06-27", "evidence": [], "reference": [ { "id": "32589600", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32589600" } ] }, { "title": "Characteristics, risk factors and outcomes among the first consecutive 1096 patients diagnosed with COVID-19 in Kuwait.", "journal": "EClinicalMedicine", "authors": "Almazeedi S, Al-Youha S, Jamal MH, Al-Haddad M, Al-Muhaini A, Al-Ghimlas F, Al-Sabah S", "date": "2020-08-09", "evidence": [], "reference": [ { "id": "32766546", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32766546" } ] } ], "biomarker_canonical_id": "AN6747", "score": 1.4, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 2 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "f": "frequency", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6343-1", "biomarker_component": [ { "biomarker": "Increased NEUT count", "assessed_biomarker_entity": { "recommended_name": "Neutrophil", "synonyms": [ { "synonym": "polymorphonuclear neutrophil" }, { "synonym": "poly" }, { "synonym": "PMN" }, { "synonym": "neutrophilic leucocyte" }, { "synonym": "polynuclear neutrophilic leukocyte" }, { "synonym": "neutrophil leucocyte" }, { "synonym": "neutrocyte" }, { "synonym": "polymorphonuclear leucocyte" }, { "synonym": "polynuclear neutrophilic leucocyte" }, { "synonym": "polymorphonuclear leukocyte" }, { "synonym": "neutrophil leukocyte" }, { "synonym": "neutrophilic leukocyte" } ] }, "assessed_biomarker_entity_id": "CO:CL_0000775", "assessed_entity_type": "cell", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "22664-7" } ], "evidence_source": [ { "id": "32259132", "database": "Pubmed", "url": 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"3,18-diethenyl-2,7,13,17-tetramethyl-1,19-dioxo-1,10,19,22,23,24-hexahydro-21H-biline-8,12-dipropanoic acid" }, { "synonym": "bilirubin" }, { "synonym": "8,12-bis(2-carboxyethyl)-2,7,13,17-tetramethyl-3,18-divinylbiladiene-ac-1,19(21H,24H)-dione" }, { "synonym": "Bilirubin" }, { "synonym": "2,7,13,17-tetramethyl-1,19-dioxo-3,18-divinyl-1,10,19,22,23,24-hexahydro-21H-biline-8,12-dipropanoic acid" }, { "synonym": "1,10,19,22,23,24-hexahydro-2,7,13,17-tetramethyl-1,19-dioxo-3,18-divinylbiline-8,12-dipropionic acid" }, { "synonym": "bilirubin(Z,Z)" }, { "synonym": "bilirubin-IXalpha" } ] }, "assessed_biomarker_entity_id": "CHEBI:16990", "assessed_entity_type": "metabolite", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "33898-8" } ], "evidence_source": [ { "id": "32311826", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32311826", "evidence_list": [ { "evidence": "Increased levels of total bilirubin have been shown to distinguish between COVID-19 patients admitted to the ICU vs those with less severe disease." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32505227", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32505227", "evidence_list": [ { "evidence": "Other consistently reported markers in non-survivors are increased procalcitonin (PCT) and IL-6 levels, as well as increased serum urea, creatinine, cystatin C, direct bilirubin, and cholinesterase." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "monitoring" } ], "condition": { "id": "DOID:0080600", "recommended_name": { "id": "DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, "synonyms": [ { "id": "DOID:0080600", "name": "SARS-CoV-2 infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan coronavirus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "COVID19", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan seafood market pneumonia virus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019-nCoV infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019 Novel Coronavirus (2019-nCoV)", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" } ] }, "evidence_source": [ { "id": "32296824", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32296824", "evidence_list": [ { "evidence": "We found that old age, and higher serum lactate dehydrogenase, C-reactive protein, the coefficient of variation of red blood cell distribution width, blood urea nitrogen, direct bilirubin, lower albumin, are associated with severe COVID-19." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32311826", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32311826", "evidence_list": [ { "evidence": "Increased levels of total bilirubin have been shown to distinguish between COVID-19 patients admitted to the ICU vs those with less severe disease." } ], "tags": [ { "tag": "condition" }, { "tag": "best_biomarker_role" } ] }, { "id": "32505227", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32505227", "evidence_list": [ { "evidence": "Other consistently reported markers in non-survivors are increased procalcitonin (PCT) and IL-6 levels, as well as increased serum urea, creatinine, cystatin C, direct bilirubin, and cholinesterase." } ], "tags": [ { "tag": "condition" }, { "tag": "best_biomarker_role" } ] } ], "citation": [ { "title": "A Tool for Early Prediction of Severe Coronavirus Disease 2019 (COVID-19): A Multicenter Study Using the Risk Nomogram in Wuhan and Guangdong, China.", "journal": "Clinical infectious diseases : an official publication of the Infectious Diseases Society of America", "authors": "Gong J, Ou J, Qiu X, Jie Y, Chen Y, Yuan L, Cao J, Tan M, Xu W, Zheng F, Shi Y, Hu B", "date": "2020-04-17", "evidence": [], "reference": [ { "id": "32296824", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32296824" } ] }, { "title": "COVID-19 and the clinical hematology laboratory.", "journal": "International journal of laboratory hematology", "authors": "Frater JL, Zini G, d'Onofrio G, Rogers HJ", "date": "2020-04-21", "evidence": [], "reference": [ { "id": "32311826", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32311826" } ] }, { "title": "Immunology of COVID-19: Current State of the Science.", "journal": "Immunity", "authors": "Vabret N, Britton GJ, Gruber C, Hegde S, Kim J, Kuksin M, Levantovsky R, Malle L, Moreira A, Park MD, Pia L, Risson E, Saffern M, Salomé B, Esai Selvan M, Spindler MP, Tan J, van der Heide V, Gregory JK, Alexandropoulos K, Bhardwaj N, Brown BD, Greenbaum B, Gümüş ZH, Homann D, Horowitz A, Kamphorst AO, Curotto de Lafaille MA, Mehandru S, Merad M, Samstein RM, None None", "date": "2020-06-09", "evidence": [], "reference": [ { "id": "32505227", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32505227" } ] } ], "biomarker_canonical_id": "AN6347", "score": 2.4, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 2 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6348-1", "biomarker_component": [ { "biomarker": "Increased TBIL level", "assessed_biomarker_entity": { "recommended_name": "Total Bilirubin", "synonyms": [] }, "assessed_biomarker_entity_id": "NCIt:C38037", "assessed_entity_type": "metabolite", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "35672-5" } ], "evidence_source": [ { "id": "29168585", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/29168585", "evidence_list": [ { "evidence": "Elevated TBIL, DBIL, and CEA were significantly associated with poor 5-year OS in stage IV CRC patients. Moreover, DBIL could be considered as an independent prognostic biomarker for OS." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_9256" }, "synonyms": [] }, "evidence_source": [ { "id": "29168585", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/29168585", "evidence_list": [ { "evidence": "Elevated TBIL, DBIL, and CEA were significantly associated with poor 5-year OS in stage IV CRC patients. Moreover, DBIL could be considered as an independent prognostic biomarker for OS." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "The prognostic impact of serum bilirubin in stage IV colorectal cancer patients.", "journal": "Journal of clinical laboratory analysis", "authors": "Yang L, Ge LY, Yu T, Liang Y, Yin Y, Chen H", "date": "2017-11-24", "evidence": [], "reference": [ { "id": "29168585", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/29168585" } ] } ], "biomarker_canonical_id": "AN6348", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "w": "weight", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6349-1", "biomarker_component": [ { "biomarker": "increased DBIL level", "assessed_biomarker_entity": { "recommended_name": "Direct bilirubin", "synonyms": [ { "synonym": "2,17-diethenyl-1,10,19,22,23,24-hexahydro-3,7,13,18-tetramethyl-1,19-dioxo-21H-biline-8,12-dipropanoic acid" }, { "synonym": "3,18-diethenyl-2,7,13,17-tetramethyl-1,19-dioxo-1,10,19,22,23,24-hexahydro-21H-biline-8,12-dipropanoic acid" }, { "synonym": "bilirubin" }, { "synonym": "8,12-bis(2-carboxyethyl)-2,7,13,17-tetramethyl-3,18-divinylbiladiene-ac-1,19(21H,24H)-dione" }, { "synonym": "Bilirubin" }, { "synonym": "2,7,13,17-tetramethyl-1,19-dioxo-3,18-divinyl-1,10,19,22,23,24-hexahydro-21H-biline-8,12-dipropanoic acid" }, { "synonym": "1,10,19,22,23,24-hexahydro-2,7,13,17-tetramethyl-1,19-dioxo-3,18-divinylbiline-8,12-dipropionic acid" }, { "synonym": "bilirubin(Z,Z)" }, { "synonym": "bilirubin-IXalpha" } ] }, "assessed_biomarker_entity_id": "CHEBI:16990", "assessed_entity_type": "metabolite", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "35672-5" } ], "evidence_source": [ { "id": "29168585", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/29168585", "evidence_list": [ { "evidence": "Elevated TBIL, DBIL, and CEA were significantly associated with poor 5-year OS in stage IV CRC patients. Moreover, DBIL could be considered as an independent prognostic biomarker for OS." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_9256" }, "synonyms": [] }, "evidence_source": [ { "id": "29168585", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/29168585", "evidence_list": [ { "evidence": "Elevated TBIL, DBIL, and CEA were significantly associated with poor 5-year OS in stage IV CRC patients. Moreover, DBIL could be considered as an independent prognostic biomarker for OS." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "The prognostic impact of serum bilirubin in stage IV colorectal cancer patients.", "journal": "Journal of clinical laboratory analysis", "authors": "Yang L, Ge LY, Yu T, Liang Y, Yin Y, Chen H", "date": "2017-11-24", "evidence": [], "reference": [ { "id": "29168585", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/29168585" } ] } ], "biomarker_canonical_id": "AN6349", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6350-1", "biomarker_component": [ { "biomarker": "increased BCHE level", "assessed_biomarker_entity": { "recommended_name": "Cholinesterase", "synonyms": [ { "synonym": "Acylcholine acylhydrolase" }, { "synonym": "Butyrylcholine esterase" }, { "synonym": "Choline esterase II" }, { "synonym": "Pseudocholinesterase" } ] }, "assessed_biomarker_entity_id": "UPKB:P06276", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "11154-2" } ], "evidence_source": [ { "id": "32505227", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32505227", "evidence_list": [ { "evidence": "Other consistently reported markers in non-survivors are increased procalcitonin (PCT) and IL-6 levels, as well as increased serum urea, creatinine, cystatin C, direct bilirubin, and cholinesterase." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:0080600", "recommended_name": { "id": "DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, "synonyms": [ { "id": "DOID:0080600", "name": "SARS-CoV-2 infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan coronavirus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "COVID19", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan seafood market pneumonia virus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019-nCoV infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019 Novel Coronavirus (2019-nCoV)", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" } ] }, "evidence_source": [ { "id": "32505227", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32505227", "evidence_list": [ { "evidence": "Other consistently reported markers in non-survivors are increased procalcitonin (PCT) and IL-6 levels, as well as increased serum urea, creatinine, cystatin C, direct bilirubin, and cholinesterase." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Immunology of COVID-19: Current State of the Science.", "journal": "Immunity", "authors": "Vabret N, Britton GJ, Gruber C, Hegde S, Kim J, Kuksin M, Levantovsky R, Malle L, Moreira A, Park MD, Pia L, Risson E, Saffern M, Salomé B, Esai Selvan M, Spindler MP, Tan J, van der Heide V, Gregory JK, Alexandropoulos K, Bhardwaj N, Brown BD, Greenbaum B, Gümüş ZH, Homann D, Horowitz A, Kamphorst AO, Curotto de Lafaille MA, Mehandru S, Merad M, Samstein RM, None None", "date": "2020-06-09", "evidence": [], "reference": [ { "id": "32505227", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32505227" } ] } ], "biomarker_canonical_id": "AN6350", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "f": "frequency", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6350-2", "biomarker_component": [ { "biomarker": "increased BCHE level", "assessed_biomarker_entity": { "recommended_name": "Cholinesterase", "synonyms": [ { "synonym": "Acylcholine acylhydrolase" }, { "synonym": "Butyrylcholine esterase" }, { "synonym": "Choline esterase II" }, { "synonym": "Pseudocholinesterase" } ] }, "assessed_biomarker_entity_id": "UPKB:P06276", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "11154-2" } ], "evidence_source": [ { "id": "30711999", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30711999", "evidence_list": [ { "evidence": "Serum concentrations of albumin, cholinesterase and total cholesterol, and total peripheral lymphocyte count (TLC) were used as nutrition related markers. Results: In multivariate analysis of nutrition related markers, serum albumin and cholinesterase levels were found to be independent prognostic indicators." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_9256" }, "synonyms": [] }, "evidence_source": [ { "id": "30711999", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30711999", "evidence_list": [ { "evidence": "Serum concentrations of albumin, cholinesterase and total cholesterol, and total peripheral lymphocyte count (TLC) were used as nutrition related markers. Results: In multivariate analysis of nutrition related markers, serum albumin and cholinesterase levels were found to be independent prognostic indicators." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Combination of Serum Albumin and Cholinesterase Levels as Prognostic Indicator in Patients ith Colorectal Cancer.", "journal": "Anticancer research", "authors": "Yamamoto M, Saito H, Uejima C, Tanio A, Tada Y, Matsunaga T, Sakamoto T, Honjo S, Ashida K, Fujiwara Y", "date": "2019-02-04", "evidence": [], "reference": [ { "id": "30711999", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30711999" } ] } ], "biomarker_canonical_id": "AN6350", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "c": "condition", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6350-3", "biomarker_component": [ { "biomarker": "increased BCHE level", "assessed_biomarker_entity": { "recommended_name": "Cholinesterase", "synonyms": [ { "synonym": "Acylcholine acylhydrolase" }, { "synonym": "Butyrylcholine esterase" }, { "synonym": "Choline esterase II" }, { "synonym": "Pseudocholinesterase" } ] }, "assessed_biomarker_entity_id": "UPKB:P06276", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "11154-2" } ], "evidence_source": [ { "id": "16233931", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/16233931", "evidence_list": [ { "evidence": "Serum cholinesterase activity was measured in diabetes, hypertensive and diabetic/hypertensive patients. The sample consisted of volunteer patients and was divided in a control group (n = 26), type 2 diabetic group (n = 16), hypertensive group (n = 12) and type 2 diabetic/hypertensive group (n = 26). In addition, blood glucose, cholesterol and triglyceride levels were determined. Serum cholinesterase activity in the control group was significantly lower in relation to the other groups (p < 0.001). Blood glucose levels were elevated in type 2 diabetic and type 2 diabetic/hypertensive groups. In vitro studies showed increased cholinesterase activity in the presence of glucose 5100 mM or insulin 0.525 UI (p < 0.001). Cholesterol and triglycerides were at normal levels only in the control group. Possibly, a relationship exists between the increase in serum cholinesterase and the vascular complications in the diabetic patients, potentially stimulated by the levels of glycemia and dyslipidemia. Although patients were receiving different medicines, the increase in enzyme activity was similar in all groups. This enzymatic profile suggests a possible interference of the diseases in the catalytic mechanism of the serum cholinesterase enzyme." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:9351", "recommended_name": { "id": "DOID:9351", "name": "diabetes mellitus", "description": "A glucose metabolism disease that is characterized by chronic hyperglycaemia with disturbances of carbohydrate, fat and protein metabolism resulting from defects in insulin secretion, insulin action, or both.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_9351" }, "synonyms": [ { "id": "DOID:9351", "name": "diabetes", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_9351" } ] }, "evidence_source": [ { "id": "16233931", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/16233931", "evidence_list": [ { "evidence": "Serum cholinesterase activity was measured in diabetes, hypertensive and diabetic/hypertensive patients. The sample consisted of volunteer patients and was divided in a control group (n = 26), type 2 diabetic group (n = 16), hypertensive group (n = 12) and type 2 diabetic/hypertensive group (n = 26). In addition, blood glucose, cholesterol and triglyceride levels were determined. Serum cholinesterase activity in the control group was significantly lower in relation to the other groups (p < 0.001). Blood glucose levels were elevated in type 2 diabetic and type 2 diabetic/hypertensive groups. In vitro studies showed increased cholinesterase activity in the presence of glucose 5100 mM or insulin 0.525 UI (p < 0.001). Cholesterol and triglycerides were at normal levels only in the control group. Possibly, a relationship exists between the increase in serum cholinesterase and the vascular complications in the diabetic patients, potentially stimulated by the levels of glycemia and dyslipidemia. Although patients were receiving different medicines, the increase in enzyme activity was similar in all groups. This enzymatic profile suggests a possible interference of the diseases in the catalytic mechanism of the serum cholinesterase enzyme." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Serum cholinesterase activity in diabetes and associated pathologies.", "journal": "Diabetes research and clinical practice", "authors": "Inácio Lunkes G, Stefanello F, Sausen Lunkes D, Maria Morsch V, Schetinger MR, Gonçalves JF", "date": "2005-10-20", "evidence": [], "reference": [ { "id": "16233931", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/16233931" } ] } ], "biomarker_canonical_id": "AN6350", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6351-1", "biomarker_component": [ { "biomarker": "decreased ALB level", "assessed_biomarker_entity": { "recommended_name": "Albumin", "synonyms": [] }, "assessed_biomarker_entity_id": "UPKB:P02768", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "35706-1" } ], "evidence_source": [ { "id": "32048163", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32048163", "evidence_list": [ { "evidence": "The combinations of the hypoalbuminemia, lymphopenia, and high concentrations of CRP and LDH in 2019-nCoV infected patients upon hospital admission may predict more severe acute lung injury." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32304745", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32304745", "evidence_list": [ { "evidence": "Decreased albumin (p <0.001), and increased lactate dehydrogenase (LDH) (p <0.001) at admission were significantly associated with severe and critical disease conditions (Table 3)." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32296824", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32296824", "evidence_list": [ { "evidence": "We found that old age, and higher serum lactate dehydrogenase, C-reactive protein, the coefficient of variation of red blood cell distribution width, blood urea nitrogen, direct bilirubin, lower albumin, are associated with severe COVID-19." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32490680", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32490680", "evidence_list": [ { "evidence": "Albumin levels could be used as an independent predictor of the risk of nonsurvivors in critically ill patients with COVID-19." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:0080600", "recommended_name": { "id": "DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, "synonyms": [ { "id": "DOID:0080600", "name": "SARS-CoV-2 infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan coronavirus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "COVID19", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan seafood market pneumonia virus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019-nCoV infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019 Novel Coronavirus (2019-nCoV)", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" } ] }, "evidence_source": [ { "id": "32048163", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32048163", "evidence_list": [ { "evidence": "The combinations of the hypoalbuminemia, lymphopenia, and high concentrations of CRP and LDH in 2019-nCoV infected patients upon hospital admission may predict more severe acute lung injury." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32304745", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32304745", "evidence_list": [ { "evidence": "Decreased albumin (p <0.001), and increased lactate dehydrogenase (LDH) (p <0.001) at admission were significantly associated with severe and critical disease conditions (Table 3)." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32296824", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32296824", "evidence_list": [ { "evidence": "We found that old age, and higher serum lactate dehydrogenase, C-reactive protein, the coefficient of variation of red blood cell distribution width, blood urea nitrogen, direct bilirubin, lower albumin, are associated with severe COVID-19." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32490680", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32490680", "evidence_list": [ { "evidence": "Albumin levels could be used as an independent predictor of the risk of nonsurvivors in critically ill patients with COVID-19." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Clinical and biochemical indexes from 2019-nCoV infected patients linked to viral loads and lung injury.", "journal": "Science China. Life sciences", "authors": "Liu Y, Yang Y, Zhang C, Huang F, Wang F, Yuan J, Wang Z, Li J, Li J, Feng C, Zhang Z, Wang L, Peng L, Chen L, Qin Y, Zhao D, Tan S, Yin L, Xu J, Zhou C, Jiang C, Liu L", "date": "2020-02-13", "evidence": [], "reference": [ { "id": "32048163", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32048163" } ] }, { "title": "Risk factors for disease severity, unimprovement, and mortality in COVID-19 patients in Wuhan, China.", "journal": "Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases", "authors": "Zhang J, Wang X, Jia X, Li J, Hu K, Chen G, Wei J, Gong Z, Zhou C, Yu H, Yu M, Lei H, Cheng F, Zhang B, Xu Y, Wang G, Dong W", "date": "2020-04-19", "evidence": [], "reference": [ { "id": "32304745", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32304745" } ] }, { "title": "A Tool for Early Prediction of Severe Coronavirus Disease 2019 (COVID-19): A Multicenter Study Using the Risk Nomogram in Wuhan and Guangdong, China.", "journal": "Clinical infectious diseases : an official publication of the Infectious Diseases Society of America", "authors": "Gong J, Ou J, Qiu X, Jie Y, Chen Y, Yuan L, Cao J, Tan M, Xu W, Zheng F, Shi Y, Hu B", "date": "2020-04-17", "evidence": [], "reference": [ { "id": "32296824", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32296824" } ] }, { "title": "Plasma albumin levels predict risk for nonsurvivors in critically ill patients with COVID-19.", "journal": "Biomarkers in medicine", "authors": "Li J, Li M, Zheng S, Li M, Zhang M, Sun M, Li X, Deng A, Cai Y, Zhang H", "date": "2020-06-04", "evidence": [], "reference": [ { "id": "32490680", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32490680" } ] } ], "biomarker_canonical_id": "AN6351", "score": 2.6, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 3 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "f": "frequency", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6351-2", "biomarker_component": [ { "biomarker": "decreased ALB level", "assessed_biomarker_entity": { "recommended_name": "Albumin", "synonyms": [] }, "assessed_biomarker_entity_id": "UPKB:P02768", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "35706-1" } ], "evidence_source": [ { "id": "32479790", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32479790", "evidence_list": [ { "evidence": "Resistant organ damage indices (albumin and albumin‚Äìglobulin ratio) were significantly associated with lower severity of COVID-19 in patients with cancer (table 3)." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "name": "COVID-19", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11054" }, "synonyms": [ { "id": "DOID:11054", "name": "tumor of the bladder", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11054" }, { "id": "DOID:11054", "name": "bladder cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11054" } ] }, "evidence_source": [ { "id": "32479790", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32479790", "evidence_list": [ { "evidence": "Resistant organ damage indices (albumin and albumin‚Äìglobulin ratio) were significantly associated with lower severity of COVID-19 in patients with cancer (table 3)." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Clinical characteristics and risk factors associated with COVID-19 disease severity in patients with cancer in Wuhan, China: a multicentre, retrospective, cohort study.", "journal": "The Lancet. Oncology", "authors": "Tian J, Yuan X, Xiao J, Zhong Q, Yang C, Liu B, Cai Y, Lu Z, Wang J, Wang Y, Liu S, Cheng B, Wang J, Zhang M, Wang L, Niu S, Yao Z, Deng X, Zhou F, Wei W, Li Q, Chen X, Chen W, Yang Q, Wu S, Fan J, Shu B, Hu Z, Wang S, Yang XP, Liu W, Miao X, Wang Z", "date": "2020-06-02", "evidence": [], "reference": [ { "id": "32479790", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32479790" } ] } ], "biomarker_canonical_id": "AN6351", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "c": "condition", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6352-1", "biomarker_component": [ { "biomarker": "increased IL-2R level", "assessed_biomarker_entity": { "recommended_name": "Interleukin-2 receptor", "synonyms": [ { "synonym": "IL-2 receptor subunit alpha" }, { "synonym": "IL-2-RA" }, { "synonym": "IL-2R subunit alpha" }, { "synonym": "IL2-RA" }, { "synonym": "TAC antigen" }, { "synonym": "p55" } ] }, "assessed_biomarker_entity_id": "UPKB:P01589", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "76039-7" } ], "evidence_source": [ { "id": "33349241", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/33349241", "evidence_list": [ { "evidence": "With following parameters such as age >67.5 years, IL2R >793.5U/mL, CRP >30.7ng/mL, ferroprotein >ug/L, WBC>9.5*10^9/L or NC >7.305*10^9/L, the progress of COVID-19 to critical stage should be closely observed and possibly prevented." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "monitoring" } ], "condition": { "id": "DOID:0080600", "recommended_name": { "id": "DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, "synonyms": [ { "id": "DOID:0080600", "name": "SARS-CoV-2 infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan coronavirus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "COVID19", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan seafood market pneumonia virus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019-nCoV infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019 Novel Coronavirus (2019-nCoV)", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" } ] }, "evidence_source": [ { "id": "33349241", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/33349241", "evidence_list": [ { "evidence": "With following parameters such as age >67.5 years, IL2R >793.5U/mL, CRP >30.7ng/mL, ferroprotein >ug/L, WBC>9.5*10^9/L or NC >7.305*10^9/L, the progress of COVID-19 to critical stage should be closely observed and possibly prevented." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Correlation analysis between disease severity and inflammation-related parameters in patients with COVID-19: a retrospective study.", "journal": "BMC infectious diseases", "authors": "Gong J, Dong H, Xia QS, Huang ZY, Wang DK, Zhao Y, Liu WH, Tu SH, Zhang MM, Wang Q, Lu FE", "date": "2020-12-23", "evidence": [], "reference": [ { "id": "33349241", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/33349241" } ] } ], "biomarker_canonical_id": "AN6352", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "w": "weight", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6352-2", "biomarker_component": [ { "biomarker": "increased IL-2R level", "assessed_biomarker_entity": { "recommended_name": "Interleukin-2 receptor", "synonyms": [ { "synonym": "IL-2 receptor subunit alpha" }, { "synonym": "IL-2-RA" }, { "synonym": "IL-2R 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Five of these 6 cases demonstrated statistically significantly increased levels of serum soluble IL-2R suggesting serum soluble IL-2R as a predictor of lymph node metastasis in early gastric cancer." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" }, "synonyms": [ { "id": "DOID:10534", "name": "gastric neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" }, { "id": "DOID:10534", "name": "gastric cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" } ] }, "evidence_source": [ { "id": "11961349", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/11961349", "evidence_list": [ { "evidence": "In 6 cases with lymph node metastasis, serum soluble IL-2R levels were significantly higher than in those without lymph node metastasis. Five of these 6 cases demonstrated statistically significantly increased levels of serum soluble IL-2R suggesting serum soluble IL-2R as a predictor of lymph node metastasis in early gastric cancer." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Serum soluble interleukin-2 receptor as a predictor of lymph node metastasis in early gastric cancer.", "journal": "Digestive surgery", "authors": "Murakami S, Sakata H, Tsuji Y, Okubo K, Hamada S, Hirayama R", "date": "2002-04-19", "evidence": [], "reference": [ { "id": "11961349", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/11961349" } ] } ], "biomarker_canonical_id": "AN6352", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "c": "condition", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6353-1", "biomarker_component": [ { "biomarker": "increased ferroprotein levels", "assessed_biomarker_entity": { "recommended_name": "Ferritin", "synonyms": [ { "synonym": "Ferritin H subunit" }, { "synonym": "Cell proliferation-inducing gene 15 protein" } ] }, "assessed_biomarker_entity_id": "UPKB:P02794", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "21418-9" } ], "evidence_source": [ { "id": "33349241", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/33349241", "evidence_list": [ { "evidence": "Significant correlations were found about age, IL2R, IL-6, IL-8, IL-10, TNFα, CRP, ferroprotein, PCT, LC, NC, and EC. PCT (R = -0.650), CRP (R = -0.604), NC (R = -0.585), age (R = -0.564), LC (R = 0.56), IL-6 (R = -0.535), IL2R (R = -0.534) and ferroprotein (R = -0.508) were highly correlated" } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "monitoring" } ], "condition": { "id": "DOID:0080600", "recommended_name": { "id": "DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, "synonyms": [ { "id": "DOID:0080600", "name": "SARS-CoV-2 infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan coronavirus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "COVID19", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan seafood market pneumonia virus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019-nCoV infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019 Novel Coronavirus (2019-nCoV)", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" } ] }, "evidence_source": [ { "id": "33349241", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/33349241", "evidence_list": [ { "evidence": "Significant correlations were found about age, IL2R, IL-6, IL-8, IL-10, TNFα, CRP, ferroprotein, PCT, LC, NC, and EC. PCT (R = -0.650), CRP (R = -0.604), NC (R = -0.585), age (R = -0.564), LC (R = 0.56), IL-6 (R = -0.535), IL2R (R = -0.534) and ferroprotein (R = -0.508) were highly correlated" } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Correlation analysis between disease severity and inflammation-related parameters in patients with COVID-19: a retrospective study.", "journal": "BMC infectious diseases", "authors": "Gong J, Dong H, Xia QS, Huang ZY, Wang DK, Zhao Y, Liu WH, Tu SH, Zhang MM, Wang Q, Lu FE", "date": "2020-12-23", "evidence": [], "reference": [ { "id": "33349241", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/33349241" } ] } ], "biomarker_canonical_id": "AN6353", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "w": "weight", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6354-1", "biomarker_component": [ { "biomarker": "increased TNFα levels", "assessed_biomarker_entity": { "recommended_name": "Tumor necrosis factor α", "synonyms": [ { "synonym": "Cachectin" }, { "synonym": "TNF-alpha" }, { "synonym": "Tumor necrosis factor ligand superfamily member 2" }, { "synonym": "TNF-a" } ] }, "assessed_biomarker_entity_id": "UPKB:P01375", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "21418-9" } ], "evidence_source": [ { "id": "33349241", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/33349241", "evidence_list": [ { "evidence": "Significant correlations were found about age, IL2R, IL-6, IL-8, IL-10, TNFα, CRP, ferroprotein, PCT, LC, NC, and EC. PCT (R = -0.650), CRP (R = -0.604), NC (R = -0.585), age (R = -0.564), LC (R = 0.56), IL-6 (R = -0.535), IL2R (R = -0.534) and ferroprotein (R = -0.508) were highly correlated" } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] }, { "biomarker": "increased TNF-α levels", "assessed_biomarker_entity": { "recommended_name": "Tumor Necrosis Factor-alpha", "synonyms": [ { "synonym": "Cachectin" }, { "synonym": "TNF-alpha" }, { "synonym": "Tumor necrosis factor ligand superfamily member 2" }, { "synonym": "TNF-a" } ] }, "assessed_biomarker_entity_id": "UPKB:P01375", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "82334-4" } ], "evidence_source": [ { "id": "32576222", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32576222", "evidence_list": [ { "evidence": "Levels of VEGF-D, TNF-alpha, SCF, LIF, IL-2, IL-4, IL-6, IL-8, IL-10, IL-15, IL-17A, IL-18, IL-1 beta, and IFN-gamma were significantly higher in the critical group than in the severe group (Table 1)." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "monitoring" } ], "condition": { "id": "DOID:0080600", "recommended_name": { "id": "DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, "synonyms": [ { "id": "DOID:0080600", "name": "SARS-CoV-2 infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan coronavirus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "COVID19", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan seafood market pneumonia virus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019-nCoV infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019 Novel Coronavirus (2019-nCoV)", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" } ] }, "evidence_source": [ { "id": "33349241", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/33349241", "evidence_list": [ { "evidence": "Significant correlations were found about age, IL2R, IL-6, IL-8, IL-10, TNFα, CRP, ferroprotein, PCT, LC, NC, and EC. PCT (R = -0.650), CRP (R = -0.604), NC (R = -0.585), age (R = -0.564), LC (R = 0.56), IL-6 (R = -0.535), IL2R (R = -0.534) and ferroprotein (R = -0.508) were highly correlated" } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32576222", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32576222", "evidence_list": [ { "evidence": "Levels of VEGF-D, TNF-alpha, SCF, LIF, IL-2, IL-4, IL-6, IL-8, IL-10, IL-15, IL-17A, IL-18, IL-1 beta, and IFN-gamma were significantly higher in the critical group than in the severe group (Table 1)." } ], "tags": [ { "tag": "condition" }, { "tag": "best_biomarker_role" } ] } ], "citation": [ { "title": "Correlation analysis between disease severity and inflammation-related parameters in patients with COVID-19: a retrospective study.", "journal": "BMC infectious diseases", "authors": "Gong J, Dong H, Xia QS, Huang ZY, Wang DK, Zhao Y, Liu WH, Tu SH, Zhang MM, Wang Q, Lu FE", "date": "2020-12-23", "evidence": [], "reference": [ { "id": "33349241", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/33349241" } ] }, { "title": "VEGF-D: a novel biomarker for detection of COVID-19 progression.", "journal": "Critical care (London, England)", "authors": "Kong Y, Han J, Wu X, Zeng H, Liu J, Zhang H", "date": "2020-06-25", "evidence": [], "reference": [ { "id": "32576222", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32576222" } ] } ], "biomarker_canonical_id": "AN6354", "score": 2.2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 1 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6748-1", "biomarker_component": [ { "biomarker": "increased IL8 level", "assessed_biomarker_entity": { "recommended_name": "Interleukin-8", "synonyms": [ { "synonym": "IL-8" }, { "synonym": "C-X-C motif chemokine 8" }, { "synonym": "Chemokine (C-X-C motif) ligand 8" }, { "synonym": "Emoctakin" }, { "synonym": "Granulocyte chemotactic protein 1" }, { "synonym": "GCP-1" }, { "synonym": "Monocyte-derived neutrophil chemotactic factor" }, { "synonym": "MDNCF" }, { "synonym": "Monocyte-derived neutrophil-activating peptide" }, { "synonym": "MONAP" }, { "synonym": "Neutrophil-activating protein 1" }, { "synonym": "NAP-1" }, { "synonym": "Protein 3-10C" }, { "synonym": "T-cell chemotactic factor" } ] }, "assessed_biomarker_entity_id": "UPKB:P10145", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "33211-4" } ], "evidence_source": [ { "id": "33349241", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/33349241", "evidence_list": [ { "evidence": "Significant correlations were found about age, IL2R, IL-6, IL-8, IL-10, TNFα, CRP, ferroprotein, PCT, LC, NC, and EC. PCT (R = -0.650), CRP (R = -0.604), NC (R = -0.585), age (R = -0.564), LC (R = 0.56), IL-6 (R = -0.535), IL2R (R = -0.534) and ferroprotein (R = -0.508) were highly correlated." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32511562", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32511562", "evidence_list": [ { "evidence": "COVID-19 is associated with high levels of [IL-6, TNF-a, IL-1b, and CXCL8/IL-8]. We found that high serum IL-6, IL-8, and TNF alpha levels at the time of hospitalization were strong and independent predictors of patient survival." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] }, { "biomarker": "increased IL8 level", "assessed_biomarker_entity": { "recommended_name": "Interleukin-8", "synonyms": [ { "synonym": "IL-8" }, { "synonym": "C-X-C motif chemokine 8" }, { "synonym": "Chemokine (C-X-C motif) ligand 8" }, { "synonym": "Emoctakin" }, { "synonym": "Granulocyte chemotactic protein 1" }, { "synonym": "GCP-1" }, { "synonym": "Monocyte-derived neutrophil chemotactic factor" }, { "synonym": "MDNCF" }, { "synonym": "Monocyte-derived neutrophil-activating peptide" }, { "synonym": "MONAP" }, { "synonym": "Neutrophil-activating protein 1" }, { "synonym": "NAP-1" }, { "synonym": "Protein 3-10C" }, { "synonym": "T-cell chemotactic factor" } ] }, "assessed_biomarker_entity_id": "UPKB: P10145", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "33211-4" } ], "evidence_source": [ { "id": "32576222", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32576222", "evidence_list": [ { "evidence": "Levels of VEGF-D, TNF-alpha, SCF, LIF, IL-2, IL-4, IL-6, IL-8, IL-10, IL-15, IL-17A, IL-18, IL-1 beta, and IFN-gamma were significantly higher in the critical group than in the severe group (Table 1)." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "monitoring" } ], "condition": { "id": "DOID:0080600", "recommended_name": { "id": "DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, "synonyms": [ { "id": "DOID:0080600", "name": "SARS-CoV-2 infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan coronavirus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "COVID19", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan seafood market pneumonia virus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019-nCoV infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019 Novel Coronavirus (2019-nCoV)", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" } ] }, "evidence_source": [ { "id": "33349241", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/33349241", "evidence_list": [ { "evidence": "Significant correlations were found about age, IL2R, IL-6, IL-8, IL-10, TNFα, CRP, ferroprotein, PCT, LC, NC, and EC. PCT (R = -0.650), CRP (R = -0.604), NC (R = -0.585), age (R = -0.564), LC (R = 0.56), IL-6 (R = -0.535), IL2R (R = -0.534) and ferroprotein (R = -0.508) were highly correlated." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32511562", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32511562", "evidence_list": [ { "evidence": "COVID-19 is associated with high levels of [IL-6, TNF-a, IL-1b, and CXCL8/IL-8]. We found that high serum IL-6, IL-8, and TNF alpha levels at the time of hospitalization were strong and independent predictors of patient survival." } ], "tags": [ { "tag": "condition" }, { "tag": "best_biomarker_role" } ] }, { "id": "32576222", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32576222", "evidence_list": [ { "evidence": "Levels of VEGF-D, TNF-alpha, SCF, LIF, IL-2, IL-4, IL-6, IL-8, IL-10, IL-15, IL-17A, IL-18, IL-1 beta, and IFN-gamma were significantly higher in the critical group than in the severe group (Table 1)." } ], "tags": [ { "tag": "condition" }, { "tag": "best_biomarker_role" } ] } ], "citation": [ { "title": "Correlation analysis between disease severity and inflammation-related parameters in patients with COVID-19: a retrospective study.", "journal": "BMC infectious diseases", "authors": "Gong J, Dong H, Xia QS, Huang ZY, Wang DK, Zhao Y, Liu WH, Tu SH, Zhang MM, Wang Q, Lu FE", "date": "2020-12-23", "evidence": [], "reference": [ { "id": "33349241", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/33349241" } ] }, { "title": "An inflammatory cytokine signature helps predict COVID-19 severity and death.", "journal": "medRxiv : the preprint server for health sciences", "authors": "Del Valle DM, Kim-Schulze S, Hsin-Hui H, Beckmann ND, Nirenberg S, Wang B, Lavin Y, Swartz T, Madduri D, Stock A, Marron T, Xie H, Patel MK, van Oekelen O, Rahman A, Kovatch P, Aberg J, Schadt E, Jagannath S, Mazumdar M, Charney A, Firpo-Betancourt A, Mendu DR, Jhang J, Reich D, Sigel K, Cordon-Cardo C, Feldmann M, Parekh S, Merad M, Gnjatic S", "date": "2020-06-09", "evidence": [], "reference": [ { "id": "32511562", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32511562" } ] }, { "title": "VEGF-D: a novel biomarker for detection of COVID-19 progression.", "journal": "Critical care (London, England)", "authors": "Kong Y, Han J, Wu X, Zeng H, Liu J, Zhang H", "date": "2020-06-25", "evidence": [], "reference": [ { "id": "32576222", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32576222" } ] } ], "biomarker_canonical_id": "AN6748", "score": 2.4, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 2 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "w": "weight", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6357-1", "biomarker_component": [ { "biomarker": "increased NEUT count", "assessed_biomarker_entity": { "recommended_name": "Neutrophil", "synonyms": [ { "synonym": "polymorphonuclear neutrophil" }, { "synonym": "poly" }, { "synonym": "PMN" }, { "synonym": "neutrophilic leucocyte" }, { "synonym": "polynuclear neutrophilic leukocyte" }, { "synonym": "neutrophil leucocyte" }, { "synonym": "neutrocyte" }, { "synonym": "polymorphonuclear leucocyte" }, { "synonym": "polynuclear neutrophilic leucocyte" }, { "synonym": "polymorphonuclear leukocyte" }, { "synonym": "neutrophil leukocyte" }, { "synonym": "neutrophilic leukocyte" } ] }, "assessed_biomarker_entity_id": "CO:CL_0000775", "assessed_entity_type": "cell", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "21418-9" } ], "evidence_source": [ { "id": "32479790", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32479790", "evidence_list": [ { "evidence": "Pro-inflammatory and infection-related biomarkers, including TNF-alpha, IL-6, procalcitonin, and C-reactive protein, as well as organ damage indices (leucocytes, neutrophils, and lactate dehydrogenase), coagulation-related indicators (D-dimer, prothrombin time, and activated partial thromboplastin time), and NT-proBNP were significantly associated with worse severity of COVID-19 in patients with cancer (table 3)." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32357994", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32357994", "evidence_list": [ { "evidence": "Post-COVID-19 infection, lower hemoglobin levels, higher total white blood cell (WBC) counts, and higher absolute neutrophil counts were associated with increased mortality (Table 3). Analysis of other serologic biomarkers demonstrated that elevated D-dimer, lactate, and lactate dehydrogenase (LDH) in patients were significantly correlated with dying (Table 3)." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "name": "COVID-19", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11054" }, "synonyms": [ { "id": "DOID:11054", "name": "tumor of the bladder", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11054" }, { "id": "DOID:11054", "name": "bladder cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11054" } ] }, "evidence_source": [ { "id": "32479790", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32479790", "evidence_list": [ { "evidence": "Pro-inflammatory and infection-related biomarkers, including TNF-alpha, IL-6, procalcitonin, and C-reactive protein, as well as organ damage indices (leucocytes, neutrophils, and lactate dehydrogenase), coagulation-related indicators (D-dimer, prothrombin time, and activated partial thromboplastin time), and NT-proBNP were significantly associated with worse severity of COVID-19 in patients with cancer (table 3)." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32357994", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32357994", "evidence_list": [ { "evidence": "Post-COVID-19 infection, lower hemoglobin levels, higher total white blood cell (WBC) counts, and higher absolute neutrophil counts were associated with increased mortality (Table 3). Analysis of other serologic biomarkers demonstrated that elevated D-dimer, lactate, and lactate dehydrogenase (LDH) in patients were significantly correlated with dying (Table 3)." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Clinical characteristics and risk factors associated with COVID-19 disease severity in patients with cancer in Wuhan, China: a multicentre, retrospective, cohort study.", "journal": "The Lancet. Oncology", "authors": "Tian J, Yuan X, Xiao J, Zhong Q, Yang C, Liu B, Cai Y, Lu Z, Wang J, Wang Y, Liu S, Cheng B, Wang J, Zhang M, Wang L, Niu S, Yao Z, Deng X, Zhou F, Wei W, Li Q, Chen X, Chen W, Yang Q, Wu S, Fan J, Shu B, Hu Z, Wang S, Yang XP, Liu W, Miao X, Wang Z", "date": "2020-06-02", "evidence": [], "reference": [ { "id": "32479790", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32479790" } ] }, { "title": "Case Fatality Rate of Cancer Patients with COVID-19 in a New York Hospital System.", "journal": "Cancer discovery", "authors": "Mehta V, Goel S, Kabarriti R, Cole D, Goldfinger M, Acuna-Villaorduna A, Pradhan K, Thota R, Reissman S, Sparano JA, Gartrell BA, Smith RV, Ohri N, Garg M, Racine AD, Kalnicki S, Perez-Soler R, Halmos B, Verma A", "date": "2020-05-03", "evidence": [], "reference": [ { "id": "32357994", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32357994" } ] } ], "biomarker_canonical_id": "AN6357", "score": 2.2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 1 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "f": "frequency", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6358-1", "biomarker_component": [ { "biomarker": "increased MONO count", "assessed_biomarker_entity": { "recommended_name": "Monocyte", "synonyms": [] }, "assessed_biomarker_entity_id": "CO:CL_0000576", "assessed_entity_type": "cell", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "27823973", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/27823973", "evidence_list": [ { "evidence": "Serum monocyte fraction were significantly associated with high Gleason score prostate cancer. The number of white blood cell count was a lot higher in patients with a Gleason score higher than 7 prostate cancer than in patients without it. Suggesting an interaction of monocytes with the progression of prostate cancer. Serum monocyte fraction was also significantly higher in men with Gleason score prostate cancer than in men with negative biopsy and Gleason score prostate cancer in the cohort of men." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "predictive" } ], "condition": { "id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, "synonyms": [ { "id": "DOID:10283", "name": "prostate neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "NGP - new growth of prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "tumor of the prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostate cancer, familial", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostatic neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "malignant tumor of the prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "hereditary prostate cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostatic cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" } ] }, "evidence_source": [ { "id": "27823973", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/27823973", "evidence_list": [ { "evidence": "Serum monocyte fraction were significantly associated with high Gleason score prostate cancer. The number of white blood cell count was a lot higher in patients with a Gleason score higher than 7 prostate cancer than in patients without it. Suggesting an interaction of monocytes with the progression of prostate cancer. Serum monocyte fraction was also significantly higher in men with Gleason score prostate cancer than in men with negative biopsy and Gleason score prostate cancer in the cohort of men." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Serum monocyte fraction of white blood cells is increased in patients with high Gleason score prostate cancer.", "journal": "Oncotarget", "authors": "Hayashi T, Fujita K, Tanigawa G, Kawashima A, Nagahara A, Ujike T, Uemura M, Takao T, Yamaguchi S, Nonomura N", "date": "2016-11-09", "evidence": [], "reference": [ { "id": "27823973", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/27823973" } ] } ], "biomarker_canonical_id": "AN6358", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "c": "condition", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6359-1", "biomarker_component": [ { "biomarker": "decreased MONO count", "assessed_biomarker_entity": { "recommended_name": "Monocyte", "synonyms": [] }, "assessed_biomarker_entity_id": "CO:CL_0000576", "assessed_entity_type": "cell", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "26484-6" } ], "evidence_source": [ { "id": "32161940", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32161940", "evidence_list": [ { "evidence": "Severe cases tend to have lower lymphocytes counts, higher leukocyte counts and neutrophil-lymphocyte-ratio (NLR), as well as lower percentages of monocytes, eosinophils, and basophils. Most of severe cases demonstrated elevated levels of infection-related biomarkers and inflammatory cytokines. The number of T cells significantly decreased, and more hampered in severe cases. Both helper T cells and suppressor T cells in patients with COVID-19 were below normal levels, and lower level of helper T cells in severe group. The percentage of naive helper T cells increased and memory helper T cells decreased in severe cases. Patients with COVID-19 also have lower level of regulatory T cells, and more obviously damaged in severe cases." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "monitoring" } ], "condition": { "id": "DOID:0080600", "recommended_name": { "id": "DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, "synonyms": [ { "id": "DOID:0080600", "name": "SARS-CoV-2 infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan coronavirus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "COVID19", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan seafood market pneumonia virus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019-nCoV infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019 Novel Coronavirus (2019-nCoV)", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" } ] }, "evidence_source": [ { "id": "32161940", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32161940", "evidence_list": [ { "evidence": "Severe cases tend to have lower lymphocytes counts, higher leukocyte counts and neutrophil-lymphocyte-ratio (NLR), as well as lower percentages of monocytes, eosinophils, and basophils. Most of severe cases demonstrated elevated levels of infection-related biomarkers and inflammatory cytokines. The number of T cells significantly decreased, and more hampered in severe cases. Both helper T cells and suppressor T cells in patients with COVID-19 were below normal levels, and lower level of helper T cells in severe group. The percentage of naive helper T cells increased and memory helper T cells decreased in severe cases. Patients with COVID-19 also have lower level of regulatory T cells, and more obviously damaged in severe cases." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Dysregulation of Immune Response in Patients With Coronavirus 2019 (COVID-19) in Wuhan, China.", "journal": "Clinical infectious diseases : an official publication of the Infectious Diseases Society of America", "authors": "Qin C, Zhou L, Hu Z, Zhang S, Yang S, Tao Y, Xie C, Ma K, Shang K, Wang W, Tian DS", "date": "2020-03-13", "evidence": [], "reference": [ { "id": "32161940", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32161940" } ] } ], "biomarker_canonical_id": "AN6359", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "c": "condition", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6358-2", "biomarker_component": [ { "biomarker": "increased MONO count", "assessed_biomarker_entity": { "recommended_name": "Monocyte", "synonyms": [] }, "assessed_biomarker_entity_id": "CO:CL_0000576", "assessed_entity_type": "cell", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "26484-6" } ], "evidence_source": [ { "id": "25814648", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/25814648", "evidence_list": [ { "evidence": "This monocyte signature was expressed at early disease onset, remained robust over the course of disease progression, and was specific for the monocytic fraction of mononuclear cells. The identified distinct signature in tumour-educated monocytes might be used as a candidate biomarker in CRC diagnosis and harbours the potential for disease follow-up and therapeutic monitoring." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_9256" }, "synonyms": [] }, "evidence_source": [ { "id": "25814648", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/25814648", "evidence_list": [ { "evidence": "This monocyte signature was expressed at early disease onset, remained robust over the course of disease progression, and was specific for the monocytic fraction of mononuclear cells. The identified distinct signature in tumour-educated monocytes might be used as a candidate biomarker in CRC diagnosis and harbours the potential for disease follow-up and therapeutic monitoring." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Tumour-educated circulating monocytes are powerful candidate biomarkers for diagnosis and disease follow-up of colorectal cancer.", "journal": "Gut", "authors": "Hamm A, Prenen H, Van Delm W, Di Matteo M, Wenes M, Delamarre E, Schmidt T, Weitz J, Sarmiento R, Dezi A, Gasparini G, Rothé F, Schmitz R, D'Hoore A, Iserentant H, Hendlisz A, Mazzone M", "date": "2015-03-31", "evidence": [], "reference": [ { "id": "25814648", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/25814648" } ] } ], "biomarker_canonical_id": "AN6358", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "w": "weight", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6360-1", "biomarker_component": [ { "biomarker": "Increased calprotectin levels", "assessed_biomarker_entity": { "recommended_name": "S100A8/S100A9", "synonyms": [] }, "assessed_biomarker_entity_id": "UPKB:P05109", "assessed_entity_type": "cell", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "26484-6" } ], "evidence_source": [ { "id": "32810439", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32810439", "evidence_list": [ { "evidence": "We performed high dimensional flow cytometry and single cell RNA sequencing of COVID-19 patient peripheral blood cells and detected the disappearance of non-classical CD14LowCD16High monocytes, the accumulation of HLA-DRLow classical monocytes, and the release of massive amounts of calprotectin (S100A8/S100A9) in severe cases. Immature CD10LowCD101-CXCR4+/- neutrophils with an immuno-suppressive profile accumulated as well in blood and lungs, suggesting emergency myelopoiesis. We finally showed that calprotectin plasma level and a routine flow cytometry assay detecting decreased frequencies of non-classical monocytes could discriminate patients who develop a severe COVID-19 form, suggesting a predictive value that deserves prospective evaluation." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:9351", "recommended_name": { "id": "DOID:9351", "name": "diabetes mellitus", "description": "A glucose metabolism disease that is characterized by chronic hyperglycaemia with disturbances of carbohydrate, fat and protein metabolism resulting from defects in insulin secretion, insulin action, or both.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_9351" }, "synonyms": [ { "id": "DOID:9351", "name": "diabetes", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_9351" } ] }, "evidence_source": [ { "id": "32810439", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32810439", "evidence_list": [ { "evidence": "We performed high dimensional flow cytometry and single cell RNA sequencing of COVID-19 patient peripheral blood cells and detected the disappearance of non-classical CD14LowCD16High monocytes, the accumulation of HLA-DRLow classical monocytes, and the release of massive amounts of calprotectin (S100A8/S100A9) in severe cases. Immature CD10LowCD101-CXCR4+/- neutrophils with an immuno-suppressive profile accumulated as well in blood and lungs, suggesting emergency myelopoiesis. 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Immature CD10LowCD101-CXCR4+/- neutrophils with an immuno-suppressive profile accumulated as well in blood and lungs, suggesting emergency myelopoiesis. 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Immature CD10LowCD101-CXCR4+/- neutrophils with an immuno-suppressive profile accumulated as well in blood and lungs, suggesting emergency myelopoiesis. 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Immature CD10LowCD101-CXCR4+/- neutrophils with an immuno-suppressive profile accumulated as well in blood and lungs, suggesting emergency myelopoiesis. 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Immature CD10LowCD101-CXCR4+/- neutrophils with an immuno-suppressive profile accumulated as well in blood and lungs, suggesting emergency myelopoiesis. 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Most of severe cases demonstrated elevated levels of infection-related biomarkers and inflammatory cytokines. The number of T cells significantly decreased, and more hampered in severe cases. Both helper T cells and suppressor T cells in patients with COVID-19 were below normal levels, and lower level of helper T cells in severe group. The percentage of naive helper T cells increased and memory helper T cells decreased in severe cases. Patients with COVID-19 also have lower level of regulatory T cells, and more obviously damaged in severe cases." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Dysregulation of Immune Response in Patients With Coronavirus 2019 (COVID-19) in Wuhan, China.", "journal": "Clinical infectious diseases : an official publication of the Infectious Diseases Society of America", "authors": "Qin C, Zhou L, Hu Z, Zhang S, Yang S, Tao Y, Xie C, Ma K, Shang K, Wang W, Tian DS", "date": "2020-03-13", "evidence": [], "reference": [ { "id": "32161940", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32161940" } ] } ], "biomarker_canonical_id": "AN6363", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "f": "frequency", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6364-1", "biomarker_component": [ { "biomarker": "increased TH count", "assessed_biomarker_entity": { "recommended_name": "Helper T cell", "synonyms": [ { "synonym": "helper T-lymphocyte" }, { "synonym": "helper T lymphocyte" }, { "synonym": "helper T-cell" }, { "synonym": "T-helper cell" } ] }, "assessed_biomarker_entity_id": "CO:CL_0000912", "assessed_entity_type": "cell", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "65758-5" } ], "evidence_source": [ { "id": "31270583", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31270583", "evidence_list": [ { "evidence": "Our results demonstrate that circulating CXCR5-PD-1hi Tph cells are associated with progression to clinical type 1 diabetes. Consequently, Tph cells could have potential both as a biomarker of disease progression and as a target for immunotherapy in type 1 diabetes." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:9351", "recommended_name": { "id": "DOID:9351", "name": "diabetes mellitus", "description": "A glucose metabolism disease that is characterized by chronic hyperglycaemia with disturbances of carbohydrate, fat and protein metabolism resulting from defects in insulin secretion, insulin action, or both.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_9351" }, "synonyms": [ { "id": "DOID:9351", "name": "diabetes", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_9351" } ] }, "evidence_source": [ { "id": "31270583", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31270583", "evidence_list": [ { "evidence": "Our results demonstrate that circulating CXCR5-PD-1hi Tph cells are associated with progression to clinical type 1 diabetes. Consequently, Tph cells could have potential both as a biomarker of disease progression and as a target for immunotherapy in type 1 diabetes." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Circulating CXCR5", "journal": "Diabetologia", "authors": "Ekman I, Ihantola EL, Viisanen T, Rao DA, Näntö-Salonen K, Knip M, Veijola R, Toppari J, Ilonen J, Kinnunen T", "date": "2019-07-05", "evidence": [], "reference": [ { "id": "31270583", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31270583" } ] } ], "biomarker_canonical_id": "AN6364", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "w": "weight", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6365-1", "biomarker_component": [ { "biomarker": "increased NTH count", "assessed_biomarker_entity": { "recommended_name": "Naive Th cell", "synonyms": [ { "synonym": "naive T-cell" }, { "synonym": "naive T lymphocyte" }, { "synonym": "naive T-lymphocyte" } ] }, "assessed_biomarker_entity_id": "CO:CL_0000898", "assessed_entity_type": "cell", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "80720-6" } ], "evidence_source": [ { "id": "32161940", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32161940", "evidence_list": [ { "evidence": "Severe cases tend to have lower lymphocytes counts, higher leukocyte counts and neutrophil-lymphocyte-ratio (NLR), as well as lower percentages of monocytes, eosinophils, and basophils. Most of severe cases demonstrated elevated levels of infection-related biomarkers and inflammatory cytokines. The number of T cells significantly decreased, and more hampered in severe cases. Both helper T cells and suppressor T cells in patients with COVID-19 were below normal levels, and lower level of helper T cells in severe group. The percentage of naive helper T cells increased and memory helper T cells decreased in severe cases. Patients with COVID-19 also have lower level of regulatory T cells, and more obviously damaged in severe cases." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "monitoring" } ], "condition": { "id": "DOID:0080600", "recommended_name": { "id": "DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, "synonyms": [ { "id": "DOID:0080600", "name": "SARS-CoV-2 infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan coronavirus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "COVID19", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan seafood market pneumonia virus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019-nCoV infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019 Novel Coronavirus (2019-nCoV)", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" } ] }, "evidence_source": [ { "id": "32161940", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32161940", "evidence_list": [ { "evidence": "Severe cases tend to have lower lymphocytes counts, higher leukocyte counts and neutrophil-lymphocyte-ratio (NLR), as well as lower percentages of monocytes, eosinophils, and basophils. Most of severe cases demonstrated elevated levels of infection-related biomarkers and inflammatory cytokines. The number of T cells significantly decreased, and more hampered in severe cases. Both helper T cells and suppressor T cells in patients with COVID-19 were below normal levels, and lower level of helper T cells in severe group. The percentage of naive helper T cells increased and memory helper T cells decreased in severe cases. Patients with COVID-19 also have lower level of regulatory T cells, and more obviously damaged in severe cases." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Dysregulation of Immune Response in Patients With Coronavirus 2019 (COVID-19) in Wuhan, China.", "journal": "Clinical infectious diseases : an official publication of the Infectious Diseases Society of America", "authors": "Qin C, Zhou L, Hu Z, Zhang S, Yang S, Tao Y, Xie C, Ma K, Shang K, Wang W, Tian DS", "date": "2020-03-13", "evidence": [], "reference": [ { "id": "32161940", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32161940" } ] } ], "biomarker_canonical_id": "AN6365", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "f": "frequency", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6366-1", "biomarker_component": [ { "biomarker": "decreased NTH count", "assessed_biomarker_entity": { "recommended_name": "Naive Th cell", "synonyms": [ { "synonym": "naive T-cell" }, { "synonym": "naive T lymphocyte" }, { "synonym": "naive T-lymphocyte" } ] }, "assessed_biomarker_entity_id": "CO:CL_0000898", "assessed_entity_type": "cell", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "80720-6" } ], "evidence_source": [ { "id": "30246868", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30246868", "evidence_list": [ { "evidence": "The frequency of Treg, HLA-DRlow monocytes and naive CD4+ and CD8+ T cells as well as the ratios of CD4/HLA-DRlow monocytes and HLA-DRlow monocytes/pDC correlated with patient's overall survival. Next to Treg, HLA-DRlow monocytes and naive T cells represent prognostic markers for NSCLC patients and might be useful for monitoring of patients' responses to immunotherapies in future studies." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1324" }, "synonyms": [] }, "evidence_source": [ { "id": "30246868", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30246868", "evidence_list": [ { "evidence": "The frequency of Treg, HLA-DRlow monocytes and naive CD4+ and CD8+ T cells as well as the ratios of CD4/HLA-DRlow monocytes and HLA-DRlow monocytes/pDC correlated with patient's overall survival. Next to Treg, HLA-DRlow monocytes and naive T cells represent prognostic markers for NSCLC patients and might be useful for monitoring of patients' responses to immunotherapies in future studies." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Blood immune cell biomarkers in lung cancer.", "journal": "Clinical and experimental immunology", "authors": "Riemann D, Cwikowski M, Turzer S, Giese T, Grallert M, Schütte W, Seliger B", "date": "2018-09-25", "evidence": [], "reference": [ { "id": "30246868", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30246868" } ] } ], "biomarker_canonical_id": "AN6366", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "c": "condition", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6367-1", "biomarker_component": [ { "biomarker": "decreased MTH count", "assessed_biomarker_entity": { "recommended_name": "Memory Th cell", "synonyms": [ { "synonym": "memory T-cell" }, { "synonym": "memory T lymphocyte" }, { "synonym": "memory T-lymphocyte" } ] }, "assessed_biomarker_entity_id": "CO:CL_0000813", "assessed_entity_type": "cell", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "32161940", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32161940", "evidence_list": [ { "evidence": "Severe cases tend to have lower lymphocytes counts, higher leukocyte counts and neutrophil-lymphocyte-ratio (NLR), as well as lower percentages of monocytes, eosinophils, and basophils. Most of severe cases demonstrated elevated levels of infection-related biomarkers and inflammatory cytokines. The number of T cells significantly decreased, and more hampered in severe cases. Both helper T cells and suppressor T cells in patients with COVID-19 were below normal levels, and lower level of helper T cells in severe group. The percentage of naive helper T cells increased and memory helper T cells decreased in severe cases. Patients with COVID-19 also have lower level of regulatory T cells, and more obviously damaged in severe cases." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "monitoring" } ], "condition": { "id": "DOID:0080600", "recommended_name": { "id": "DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, "synonyms": [ { "id": "DOID:0080600", "name": "SARS-CoV-2 infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan coronavirus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "COVID19", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan seafood market pneumonia virus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019-nCoV infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019 Novel Coronavirus (2019-nCoV)", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" } ] }, "evidence_source": [ { "id": "32161940", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32161940", "evidence_list": [ { "evidence": "Severe cases tend to have lower lymphocytes counts, higher leukocyte counts and neutrophil-lymphocyte-ratio (NLR), as well as lower percentages of monocytes, eosinophils, and basophils. Most of severe cases demonstrated elevated levels of infection-related biomarkers and inflammatory cytokines. The number of T cells significantly decreased, and more hampered in severe cases. Both helper T cells and suppressor T cells in patients with COVID-19 were below normal levels, and lower level of helper T cells in severe group. The percentage of naive helper T cells increased and memory helper T cells decreased in severe cases. Patients with COVID-19 also have lower level of regulatory T cells, and more obviously damaged in severe cases." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Dysregulation of Immune Response in Patients With Coronavirus 2019 (COVID-19) in Wuhan, China.", "journal": "Clinical infectious diseases : an official publication of the Infectious Diseases Society of America", "authors": "Qin C, Zhou L, Hu Z, Zhang S, Yang S, Tao Y, Xie C, Ma K, Shang K, Wang W, Tian DS", "date": "2020-03-13", "evidence": [], "reference": [ { "id": "32161940", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32161940" } ] } ], "biomarker_canonical_id": "AN6367", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "f": "frequency", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6368-1", "biomarker_component": [ { "biomarker": "increased memory TH cell count", "assessed_biomarker_entity": { "recommended_name": "Memory Th cell", "synonyms": [ { "synonym": "memory T-cell" }, { "synonym": "memory T lymphocyte" }, { "synonym": "memory T-lymphocyte" } ] }, "assessed_biomarker_entity_id": "CO:CL_0000813", "assessed_entity_type": "cell", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "30574794", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30574794", "evidence_list": [ { "evidence": "Subjects with type 2 diabetes mellitus had elevated percentages of effector memory T cells ((CD4+CD45RO+CD62L‚Äì; 21.8% ¬± 11.2% vs 17.0% ¬± 9.2% in non-type 2 diabetes mellitus, p < 0.01) and central memory T cells (CD4+CD45RO+CD62L+; 38.0% ¬± 10.7% vs 36.0% ¬± 9.5% in non-type 2 diabetes mellitus, p < 0.01). The proportion of effector memory T cells was increased in type 2 diabetes mellitus subjects with cardiovascular disease as compared to those without (26.4% ¬± 11.5% vs 18.4% ¬± 10.2%, p < 0.05), while no difference in regulatory T cells was observed between these two patient groups. This study identifies effector memory T cells as a potential cellular biomarker for cardiovascular disease among subjects with type 2 diabetes mellitus, suggesting a state of exacerbated immune activation in type 2 diabetes mellitus patients with cardiovascular disease." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:9351", "recommended_name": { "id": "DOID:9351", "name": "diabetes mellitus", "description": "A glucose metabolism disease that is characterized by chronic hyperglycaemia with disturbances of carbohydrate, fat and protein metabolism resulting from defects in insulin secretion, insulin action, or both.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_9351" }, "synonyms": [ { "id": "DOID:9351", "name": "diabetes", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_9351" } ] }, "evidence_source": [ { "id": "30574794", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30574794", "evidence_list": [ { "evidence": "Subjects with type 2 diabetes mellitus had elevated percentages of effector memory T cells ((CD4+CD45RO+CD62L‚Äì; 21.8% ¬± 11.2% vs 17.0% ¬± 9.2% in non-type 2 diabetes mellitus, p < 0.01) and central memory T cells (CD4+CD45RO+CD62L+; 38.0% ¬± 10.7% vs 36.0% ¬± 9.5% in non-type 2 diabetes mellitus, p < 0.01). The proportion of effector memory T cells was increased in type 2 diabetes mellitus subjects with cardiovascular disease as compared to those without (26.4% ¬± 11.5% vs 18.4% ¬± 10.2%, p < 0.05), while no difference in regulatory T cells was observed between these two patient groups. This study identifies effector memory T cells as a potential cellular biomarker for cardiovascular disease among subjects with type 2 diabetes mellitus, suggesting a state of exacerbated immune activation in type 2 diabetes mellitus patients with cardiovascular disease." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Elevated circulating effector memory T cells but similar levels of regulatory T cells in patients with type 2 diabetes mellitus and cardiovascular disease.", "journal": "Diabetes & vascular disease research", "authors": "Rattik S, Engelbertsen D, Wigren M, Ljungcrantz I, Östling G, Persson M, Nordin Fredrikson G, Bengtsson E, Nilsson J, Björkbacka H", "date": "2018-12-24", "evidence": [], "reference": [ { "id": "30574794", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30574794" } ] } ], "biomarker_canonical_id": "AN6368", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "f": "frequency", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6369-1", "biomarker_component": [ { "biomarker": "decreased TREG count", "assessed_biomarker_entity": { "recommended_name": "Regulatory T cell", "synonyms": [ { "synonym": "regulatory T-cell" }, { "synonym": "regulatory T lymphocyte" }, { "synonym": "suppressor T cell" }, { "synonym": "regulatory T-lymphocyte" }, { "synonym": "suppressor T lymphocyte" }, { "synonym": "suppressor T-lymphocyte" }, { "synonym": "Treg" }, { "synonym": "suppressor T-cell" } ] }, "assessed_biomarker_entity_id": "CO:CL_0000815", "assessed_entity_type": "cell", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "90413-6" } ], "evidence_source": [ { "id": "32161940", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32161940", "evidence_list": [ { "evidence": "Severe cases tend to have lower lymphocytes counts, higher leukocyte counts and neutrophil-lymphocyte-ratio (NLR), as well as lower percentages of monocytes, eosinophils, and basophils. Most of severe cases demonstrated elevated levels of infection-related biomarkers and inflammatory cytokines. The number of T cells significantly decreased, and more hampered in severe cases. Both helper T cells and suppressor T cells in patients with COVID-19 were below normal levels, and lower level of helper T cells in severe group. The percentage of naive helper T cells increased and memory helper T cells decreased in severe cases. Patients with COVID-19 also have lower level of regulatory T cells, and more obviously damaged in severe cases." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "monitoring" } ], "condition": { "id": "DOID:0080600", "recommended_name": { "id": "DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, "synonyms": [ { "id": "DOID:0080600", "name": "SARS-CoV-2 infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan coronavirus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "COVID19", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan seafood market pneumonia virus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019-nCoV infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019 Novel Coronavirus (2019-nCoV)", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" } ] }, "evidence_source": [ { "id": "32161940", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32161940", "evidence_list": [ { "evidence": "Severe cases tend to have lower lymphocytes counts, higher leukocyte counts and neutrophil-lymphocyte-ratio (NLR), as well as lower percentages of monocytes, eosinophils, and basophils. Most of severe cases demonstrated elevated levels of infection-related biomarkers and inflammatory cytokines. The number of T cells significantly decreased, and more hampered in severe cases. Both helper T cells and suppressor T cells in patients with COVID-19 were below normal levels, and lower level of helper T cells in severe group. The percentage of naive helper T cells increased and memory helper T cells decreased in severe cases. Patients with COVID-19 also have lower level of regulatory T cells, and more obviously damaged in severe cases." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Dysregulation of Immune Response in Patients With Coronavirus 2019 (COVID-19) in Wuhan, China.", "journal": "Clinical infectious diseases : an official publication of the Infectious Diseases Society of America", "authors": "Qin C, Zhou L, Hu Z, Zhang S, Yang S, Tao Y, Xie C, Ma K, Shang K, Wang W, Tian DS", "date": "2020-03-13", "evidence": [], "reference": [ { "id": "32161940", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32161940" } ] } ], "biomarker_canonical_id": "AN6369", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "c": "condition", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6370-1", "biomarker_component": [ { "biomarker": "increased TREG count", "assessed_biomarker_entity": { "recommended_name": "Regulatory T cell", "synonyms": [ { "synonym": "regulatory T-cell" }, { "synonym": "regulatory T lymphocyte" }, { "synonym": "suppressor T cell" }, { "synonym": "regulatory T-lymphocyte" }, { "synonym": "suppressor T lymphocyte" }, { "synonym": "suppressor T-lymphocyte" }, { "synonym": "Treg" }, { "synonym": "suppressor T-cell" } ] }, "assessed_biomarker_entity_id": "CO:CL_0000815", "assessed_entity_type": "cell", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "90413-6" } ], "evidence_source": [ { "id": "27976733", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/27976733", "evidence_list": [ { "evidence": "The percentages of naive Treg were found elevated in NSCLC patients compared to HD and were associated with poor clinical outcome, whereas the percentage of terminal effector Treg was lower compared to HD and higher levels were correlated with improved clinical response. At baseline, normal levels of naive and effector Treg were associated with longer overall survival (OS) compared to high levels, while the high frequency of the terminal effector Treg was correlated with longer Progression-Free Survival and OS." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_9256" }, "synonyms": [] }, "evidence_source": [ { "id": "27976733", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/27976733", "evidence_list": [ { "evidence": "The percentages of naive Treg were found elevated in NSCLC patients compared to HD and were associated with poor clinical outcome, whereas the percentage of terminal effector Treg was lower compared to HD and higher levels were correlated with improved clinical response. At baseline, normal levels of naive and effector Treg were associated with longer overall survival (OS) compared to high levels, while the high frequency of the terminal effector Treg was correlated with longer Progression-Free Survival and OS." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Prognostic value of circulating regulatory T cell subsets in untreated non-small cell lung cancer patients.", "journal": "Scientific reports", "authors": "Kotsakis A, Koinis F, Katsarou A, Gioulbasani M, Aggouraki D, Kentepozidis N, Georgoulias V, Vetsika EK", "date": "2016-12-16", "evidence": [], "reference": [ { "id": "27976733", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/27976733" } ] } ], "biomarker_canonical_id": "AN6370", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "c": "condition", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6371-1", "biomarker_component": [ { "biomarker": "increased ESR", "assessed_biomarker_entity": { "recommended_name": "Erythrocyte sedimentation rate", "synonyms": [] }, "assessed_biomarker_entity_id": "NCIt:C74611", "assessed_entity_type": "cell", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "30341-2" } ], "evidence_source": [ { "id": "29285390", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/29285390", "evidence_list": [ { "evidence": "Elevated ESR was found to be associated with metastatic disease and was also found to be a prognostic factor adversely affecting survival in patients with cutaneous melanoma." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_4159" }, "synonyms": [ { "id": "DOID:4159", "name": "CA - skin cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_4159" }, { "id": "DOID:4159", "name": "malignant neoplasm of skin", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_4159" }, { "id": "DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_4159" } ] }, "evidence_source": [ { "id": "29285390", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/29285390", "evidence_list": [ { "evidence": "Elevated ESR was found to be associated with metastatic disease and was also found to be a prognostic factor adversely affecting survival in patients with cutaneous melanoma." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Elevated erythrocyte sedimentation rate is associated with metastatic disease and worse survival in patients with cutaneous malignant melanoma.", "journal": "Molecular and clinical oncology", "authors": "Tas F, Erturk K", "date": "2017-12-30", "evidence": [], "reference": [ { "id": "29285390", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/29285390" } ] } ], "biomarker_canonical_id": "AN6371", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "c": "condition", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6371-2", "biomarker_component": [ { "biomarker": "increased ESR", "assessed_biomarker_entity": { "recommended_name": "Erythrocyte sedimentation rate", "synonyms": [] }, "assessed_biomarker_entity_id": "NCIt:C74611", "assessed_entity_type": "cell", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "30341-2" } ], "evidence_source": [ { "id": "32503382", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32503382", "evidence_list": [ { "evidence": "Erythrocyte sedimentation rate (ESR) (R=0.55, p < .01) was positively associated with CT severity scores. To sum up, we can conclude from the analysis of published studies that hematological (lymphocyte count, neutrophil count, and NLR), inflammatory (CRP, ESR, IL-6), and especially biochemical (D-dimer, Troponins, CK) parameters correlate with severe prognosis or exitus in COVID-19 patients and can therefore be used as predictive biomarkers." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32324595", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32324595", "evidence_list": [ { "evidence": "Inflammatory biomarkers such as CRP and erythrocyte sedimentation rate were increased." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "predictive" } ], "condition": { "id": "DOID:0080600", "recommended_name": { "id": "DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, "synonyms": [ { "id": "DOID:0080600", "name": "SARS-CoV-2 infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan coronavirus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "COVID19", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan seafood market pneumonia virus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019-nCoV infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019 Novel Coronavirus (2019-nCoV)", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" } ] }, "evidence_source": [ { "id": "32503382", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32503382", "evidence_list": [ { "evidence": "Erythrocyte sedimentation rate (ESR) (R=0.55, p < .01) was positively associated with CT severity scores. To sum up, we can conclude from the analysis of published studies that hematological (lymphocyte count, neutrophil count, and NLR), inflammatory (CRP, ESR, IL-6), and especially biochemical (D-dimer, Troponins, CK) parameters correlate with severe prognosis or exitus in COVID-19 patients and can therefore be used as predictive biomarkers." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32324595", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32324595", "evidence_list": [ { "evidence": "Inflammatory biomarkers such as CRP and erythrocyte sedimentation rate were increased." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Biomarkers associated with COVID-19 disease progression.", "journal": "Critical reviews in clinical laboratory sciences", "authors": "Ponti G, Maccaferri M, Ruini C, Tomasi A, Ozben T", "date": "2020-06-07", "evidence": [], "reference": [ { "id": "32503382", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32503382" } ] }, { "title": "The laboratory tests and host immunity of COVID-19 patients with different severity of illness.", "journal": "JCI insight", "authors": "Wang F, Hou H, Luo Y, Tang G, Wu S, Huang M, Liu W, Zhu Y, Lin Q, Mao L, Fang M, Zhang H, Sun Z", "date": "2020-04-24", "evidence": [], "reference": [ { "id": "32324595", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32324595" } ] } ], "biomarker_canonical_id": "AN6371", "score": 2.2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 1 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "w": "weight", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6309-3", "biomarker_component": [ { "biomarker": "Increased TNF-α level", "assessed_biomarker_entity": { "recommended_name": "Tumor Necrosis Factor-alpha", "synonyms": [ { "synonym": "Cachectin" }, { "synonym": "TNF-alpha" }, { "synonym": "Tumor necrosis factor ligand superfamily member 2" }, { "synonym": "TNF-a" } ] }, "assessed_biomarker_entity_id": "UPKB:P01375", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "33211-4" } ], "evidence_source": [ { "id": "28791816", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/28791816", "evidence_list": [ { "evidence": "The study showed that IL-6, IL-8 and TNF-alpha levels correlated with clinical disease stage and lymph node metastasis as well as with ER and HER2 antigen expression. Specifically, IL-6 and IL-8 seem to have significant potential as prognostic cancer biomarkers." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "name": "breast cancer", "description": "A thoracic cancer that originates in the mammary gland.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, "synonyms": [ { "id": "DOID:1612", "name": "malignant tumor of the breast", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "breast tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "mammary cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "primary breast cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "mammary tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "malignant neoplasm of breast", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" } ] }, "evidence_source": [ { "id": "28791816", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/28791816", "evidence_list": [ { "evidence": "The study showed that IL-6, IL-8 and TNF-alpha levels correlated with clinical disease stage and lymph node metastasis as well as with ER and HER2 antigen expression. Specifically, IL-6 and IL-8 seem to have significant potential as prognostic cancer biomarkers." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "IL-6, IL-8 and TNF-α levels correlate with disease stage in breast cancer patients.", "journal": "Advances in clinical and experimental medicine : official organ Wroclaw Medical University", "authors": "Ma Y, Ren Y, Dai ZJ, Wu CJ, Ji YH, Xu J", "date": "2017-08-10", "evidence": [], "reference": [ { "id": "28791816", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/28791816" } ] } ], "biomarker_canonical_id": "AN6309", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "c": "condition", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6278-4", "biomarker_component": [ { "biomarker": "increased IL6 level", "assessed_biomarker_entity": { "recommended_name": "Interleukin-6", "synonyms": [ { "synonym": "IL-6" }, { "synonym": "B-cell stimulatory factor 2" }, { "synonym": "BSF-2" }, { "synonym": "CTL differentiation factor" }, { "synonym": "CDF" }, { "synonym": "Hybridoma growth factor" }, { "synonym": "Interferon beta-2" }, { "synonym": "IFN-beta-2" } ] }, "assessed_biomarker_entity_id": "UPKB:P05231", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "33211-4" } ], "evidence_source": [ { "id": "28791816", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/28791816", "evidence_list": [ { "evidence": "The study showed that IL-6, IL-8 and TNF-alpha levels correlated with clinical disease stage and lymph node metastasis as well as with ER and HER2 antigen expression. Specifically, IL-6 and IL-8 seem to have significant potential as prognostic cancer biomarkers." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "name": "breast cancer", "description": "A thoracic cancer that originates in the mammary gland.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, "synonyms": [ { "id": "DOID:1612", "name": "malignant tumor of the breast", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "breast tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "mammary cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "primary breast cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "mammary tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "malignant neoplasm of breast", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" } ] }, "evidence_source": [ { "id": "28791816", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/28791816", "evidence_list": [ { "evidence": "The study showed that IL-6, IL-8 and TNF-alpha levels correlated with clinical disease stage and lymph node metastasis as well as with ER and HER2 antigen expression. Specifically, IL-6 and IL-8 seem to have significant potential as prognostic cancer biomarkers." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "IL-6, IL-8 and TNF-α levels correlate with disease stage in breast cancer patients.", "journal": "Advances in clinical and experimental medicine : official organ Wroclaw Medical University", "authors": "Ma Y, Ren Y, Dai ZJ, Wu CJ, Ji YH, Xu J", "date": "2017-08-10", "evidence": [], "reference": [ { "id": "28791816", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/28791816" } ] } ], "biomarker_canonical_id": "AN6278", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "f": "frequency", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6372-1", "biomarker_component": [ { "biomarker": "increased IL8 level", "assessed_biomarker_entity": { "recommended_name": "Interleukin-8", "synonyms": [ { "synonym": "IL-8" }, { "synonym": "C-X-C motif chemokine 8" }, { "synonym": "Chemokine (C-X-C motif) ligand 8" }, { "synonym": "Emoctakin" }, { "synonym": "Granulocyte chemotactic protein 1" }, { "synonym": "GCP-1" }, { "synonym": "Monocyte-derived neutrophil chemotactic factor" }, { "synonym": "MDNCF" }, { "synonym": "Monocyte-derived neutrophil-activating peptide" }, { "synonym": "MONAP" }, { "synonym": "Neutrophil-activating protein 1" }, { "synonym": "NAP-1" }, { "synonym": "Protein 3-10C" }, { "synonym": "T-cell chemotactic factor" } ] }, "assessed_biomarker_entity_id": "UPKB:P10145", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "33211-4" } ], "evidence_source": [ { "id": "28791816", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/28791816", "evidence_list": [ { "evidence": "The study showed that IL-6, IL-8 and TNF-alpha levels correlated with clinical disease stage and lymph node metastasis as well as with ER and HER2 antigen expression. Specifically, IL-6 and IL-8 seem to have significant potential as prognostic cancer biomarkers." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "name": "breast cancer", "description": "A thoracic cancer that originates in the mammary gland.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, "synonyms": [ { "id": "DOID:1612", "name": "malignant tumor of the breast", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "breast tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "mammary cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "primary breast cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "mammary tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "malignant neoplasm of breast", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" } ] }, "evidence_source": [ { "id": "28791816", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/28791816", "evidence_list": [ { "evidence": "The study showed that IL-6, IL-8 and TNF-alpha levels correlated with clinical disease stage and lymph node metastasis as well as with ER and HER2 antigen expression. Specifically, IL-6 and IL-8 seem to have significant potential as prognostic cancer biomarkers." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "IL-6, IL-8 and TNF-α levels correlate with disease stage in breast cancer patients.", "journal": "Advances in clinical and experimental medicine : official organ Wroclaw Medical University", "authors": "Ma Y, Ren Y, Dai ZJ, Wu CJ, Ji YH, Xu J", "date": "2017-08-10", "evidence": [], "reference": [ { "id": "28791816", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/28791816" } ] } ], "biomarker_canonical_id": "AN6372", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "c": "condition", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6372-2", "biomarker_component": [ { "biomarker": "increased IL8 level", "assessed_biomarker_entity": { "recommended_name": "Interleukin-8", "synonyms": [ { "synonym": "IL-8" }, { "synonym": "C-X-C motif chemokine 8" }, { "synonym": "Chemokine (C-X-C motif) ligand 8" }, { "synonym": "Emoctakin" }, { "synonym": "Granulocyte chemotactic protein 1" }, { "synonym": "GCP-1" }, { "synonym": "Monocyte-derived neutrophil chemotactic factor" }, { "synonym": "MDNCF" }, { "synonym": "Monocyte-derived neutrophil-activating peptide" }, { "synonym": "MONAP" }, { "synonym": "Neutrophil-activating protein 1" }, { "synonym": "NAP-1" }, { "synonym": "Protein 3-10C" }, { "synonym": "T-cell chemotactic factor" } ] }, "assessed_biomarker_entity_id": "UPKB:P10145", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "33211-4" } ], "evidence_source": [ { "id": "28836077", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/28836077", "evidence_list": [ { "evidence": "Patients with T2D exhibited significantly higher serum IL-8 levels than non-diabetic subjects (69.27 ¬± 112.83 vs. 16.03 ¬± 24.27 pg/mL, p < 0.001). Patients with T2D display a marked elevation of circulating IL-8 levels which identify subjects with worse inflammatory, glycometabolic and lipid profile and lower vitamin D levels." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "monitoring" } ], "condition": { "id": "DOID:9351", "recommended_name": { "id": "DOID:9351", "name": "diabetes mellitus", "description": "A glucose metabolism disease that is characterized by chronic hyperglycaemia with disturbances of carbohydrate, fat and protein metabolism resulting from defects in insulin secretion, insulin action, or both.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_9351" }, "synonyms": [ { "id": "DOID:9351", "name": "diabetes", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_9351" } ] }, "evidence_source": [ { "id": "28836077", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/28836077", "evidence_list": [ { "evidence": "Patients with T2D exhibited significantly higher serum IL-8 levels than non-diabetic subjects (69.27 ¬± 112.83 vs. 16.03 ¬± 24.27 pg/mL, p < 0.001). Patients with T2D display a marked elevation of circulating IL-8 levels which identify subjects with worse inflammatory, glycometabolic and lipid profile and lower vitamin D levels." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Circulating IL-8 levels are increased in patients with type 2 diabetes and associated with worse inflammatory and cardiometabolic profile.", "journal": "Acta diabetologica", "authors": "Cimini FA, Barchetta I, Porzia A, Mainiero F, Costantino C, Bertoccini L, Ceccarelli V, Morini S, Baroni MG, Lenzi A, Cavallo MG", "date": "2017-08-25", "evidence": [], "reference": [ { "id": "28836077", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/28836077" } ] } ], "biomarker_canonical_id": "AN6372", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "f": "frequency", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6749-1", "biomarker_component": [ { "biomarker": "increased TNNI3 level", "assessed_biomarker_entity": { "recommended_name": "Cardiac troponin I", "synonyms": [ { "synonym": "Cardiac troponin I" } ] }, "assessed_biomarker_entity_id": "UPKB:P19429", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "10839-9" } ], "evidence_source": [ { "id": "32169400", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32169400", "evidence_list": [ { "evidence": "cTnI values are significantly increased in patients with severe SARS-CoV-2 infection compared to those with milder forms of disease. It is hence reasonable to hypothesize that initial measurement of cardiac damage biomarkers immediately after hospitalization for SARS-CoV-2 infection, as well as longitudinal monitoring during hospital stay, may help identifying a subset of patients with possible cardiac injury and thereby predict the progression of COVID-19 towards a worse clinical picture." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32530509", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32530509", "evidence_list": [ { "evidence": "High troponin I levels with either advanced age more than 60 years or elevated AST levels was the best model to predict poor outcomes." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32171076", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32171076", "evidence_list": [ { "evidence": "Age, comorbidities, lymphocytopenia and elevated alanine aminotransferase, d-dimer, creatine kinase, high-sensitivity cardiac troponin I, prothrombin time, and disease severity were reported to be associated with intensive care unit admission." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32475810", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32475810", "evidence_list": [ { "evidence": "A retrospective study performed in China of patients with confirmed COVID-19 based on SARS-CoV-2 RNA detection, revealed a univariable odds ratio for death at 80.1 (95% CI 10.3-620.4, p<0.0001) for hs-TnI. Another study of 416 hospitalised patients with COVID-19 reported that hs-TnI was elevated in 1 in 5 patients on presentation." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32251612", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32251612", "evidence_list": [ { "evidence": "In a cohort of 191 patients with confirmed COVID-19 based on SARS-CoV-2 RNA detection, the univariable odds ratio for death when high-sensitivity cardiac troponin I concentrations were above the 99th percentile upper reference limit was 80.1 (95% CI, 10.3-620.4; P<0.0001). This was higher than the odds ratios observed for all other biomarkers tested, including D-dimer and lymphocyte count." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] }, { "biomarker": "increased TNNI3 level", "assessed_biomarker_entity": { "recommended_name": "Cardiac Troponin I", "synonyms": [ { "synonym": "Cardiac troponin I" } ] }, "assessed_biomarker_entity_id": "UPKB:P19429", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "10839-9" } ], "evidence_source": [ { "id": "32589600", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32589600", "evidence_list": [ { "evidence": "Many biomarkers have been associated with poor outcomes and represent a candidate for risk stratification models for predicting severe COVID-19 in order to guide clinical care. Among all, lymphopenia, thrombocytopenia, leucocytosis, CRP, PCT, LDH, AST, ALT, D-dimer, cTn represent the most predictive parameters of severe COVID-19" } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32596365", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32596365", "evidence_list": [ { "evidence": "The levels of laboratory cardiac markers, lactose dehydrogenase (LDH), creatine kinase (CK), creatinine kinase-muscle/brain activity (CK-MB), myoglobin (Mb), cardiac troponin I (cTnI), alpha-hydroxybutyrate dehydrogenase (α-HBDH), aspartate aminotransferase (AST), and N-terminal of the prohormone brain natriuretic peptide (NT-proBNP) increase in different proportions in patients with COVID-19 (see Table 1)." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32209382", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32209382", "evidence_list": [ { "evidence": "This study reveals that the heart is also a major target of COVID-19 infection, and myocardial enzyme spectrum assays could help the diagnosis, prognosis and guide the treatments to prevent heart failure in COVID-19 patients. [DOI:https://doi.org/10.21203/rs.3.rs-23849/v1] We noted significantly increased cTnI, CK, HBDB and LDH levels in very severe group as compare to severe." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "monitoring" } ], "condition": { "id": "DOID:0080600", "recommended_name": { "id": "DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, "synonyms": [ { "id": "DOID:0080600", "name": "SARS-CoV-2 infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan coronavirus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "COVID19", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan seafood market pneumonia virus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019-nCoV infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019 Novel Coronavirus (2019-nCoV)", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" } ] }, "evidence_source": [ { "id": "32169400", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32169400", "evidence_list": [ { "evidence": "cTnI values are significantly increased in patients with severe SARS-CoV-2 infection compared to those with milder forms of disease. It is hence reasonable to hypothesize that initial measurement of cardiac damage biomarkers immediately after hospitalization for SARS-CoV-2 infection, as well as longitudinal monitoring during hospital stay, may help identifying a subset of patients with possible cardiac injury and thereby predict the progression of COVID-19 towards a worse clinical picture." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32530509", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32530509", "evidence_list": [ { "evidence": "High troponin I levels with either advanced age more than 60 years or elevated AST levels was the best model to predict poor outcomes." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32171076", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32171076", "evidence_list": [ { "evidence": "Age, comorbidities, lymphocytopenia and elevated alanine aminotransferase, d-dimer, creatine kinase, high-sensitivity cardiac troponin I, prothrombin time, and disease severity were reported to be associated with intensive care unit admission." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32475810", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32475810", "evidence_list": [ { "evidence": "A retrospective study performed in China of patients with confirmed COVID-19 based on SARS-CoV-2 RNA detection, revealed a univariable odds ratio for death at 80.1 (95% CI 10.3-620.4, p<0.0001) for hs-TnI. Another study of 416 hospitalised patients with COVID-19 reported that hs-TnI was elevated in 1 in 5 patients on presentation." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32251612", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32251612", "evidence_list": [ { "evidence": "In a cohort of 191 patients with confirmed COVID-19 based on SARS-CoV-2 RNA detection, the univariable odds ratio for death when high-sensitivity cardiac troponin I concentrations were above the 99th percentile upper reference limit was 80.1 (95% CI, 10.3-620.4; P<0.0001). This was higher than the odds ratios observed for all other biomarkers tested, including D-dimer and lymphocyte count." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32589600", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32589600", "evidence_list": [ { "evidence": "Many biomarkers have been associated with poor outcomes and represent a candidate for risk stratification models for predicting severe COVID-19 in order to guide clinical care. Among all, lymphopenia, thrombocytopenia, leucocytosis, CRP, PCT, LDH, AST, ALT, D-dimer, cTn represent the most predictive parameters of severe COVID-19" } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32596365", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32596365", "evidence_list": [ { "evidence": "The levels of laboratory cardiac markers, lactose dehydrogenase (LDH), creatine kinase (CK), creatinine kinase-muscle/brain activity (CK-MB), myoglobin (Mb), cardiac troponin I (cTnI), alpha-hydroxybutyrate dehydrogenase (α-HBDH), aspartate aminotransferase (AST), and N-terminal of the prohormone brain natriuretic peptide (NT-proBNP) increase in different proportions in patients with COVID-19 (see Table 1)." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32209382", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32209382", "evidence_list": [ { "evidence": "This study reveals that the heart is also a major target of COVID-19 infection, and myocardial enzyme spectrum assays could help the diagnosis, prognosis and guide the treatments to prevent heart failure in COVID-19 patients. [DOI:https://doi.org/10.21203/rs.3.rs-23849/v1] We noted significantly increased cTnI, CK, HBDB and LDH levels in very severe group as compare to severe." } ], "tags": [ { "tag": "condition" }, { "tag": "best_biomarker_role" } ] } ], "citation": [ { "title": "Cardiac troponin I in patients with coronavirus disease 2019 (COVID-19): Evidence from a meta-analysis.", "journal": "Progress in cardiovascular diseases", "authors": "Lippi G, Lavie CJ, Sanchis-Gomar F", "date": "2020-03-15", "evidence": [], "reference": [ { "id": "32169400", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32169400" } ] }, { "title": "Association of cardiac biomarkers and comorbidities with increased mortality, severity, and cardiac injury in COVID-19 patients: A meta-regression and decision tree analysis.", "journal": "Journal of medical virology", "authors": "Toraih EA, Elshazli RM, Hussein MH, Elgaml A, Amin M, El-Mowafy M, El-Mesery M, Ellythy A, Duchesne J, Killackey MT, Ferdinand KC, Kandil E, Fawzy MS", "date": "2020-06-13", "evidence": [], "reference": [ { "id": "32530509", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32530509" } ] }, { "title": "Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: a retrospective cohort study.", "journal": "Lancet (London, England)", "authors": "Zhou F, Yu T, Du R, Fan G, Liu Y, Liu Z, Xiang J, Wang Y, Song B, Gu X, Guan L, Wei Y, Li H, Wu X, Xu J, Tu S, Zhang Y, Chen H, Cao B", "date": "2020-03-15", "evidence": [], "reference": [ { "id": "32171076", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32171076" } ] }, { "title": "The role of biomarkers in diagnosis of COVID-19 - A systematic review.", "journal": "Life sciences", "authors": "Kermali M, Khalsa RK, Pillai K, Ismail Z, Harky A", "date": "2020-06-02", "evidence": [], "reference": [ { "id": "32475810", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32475810" } ] }, { "title": "High-Sensitivity Cardiac Troponin Can Be an Ally in the Fight Against COVID-19.", "journal": "Circulation", "authors": "Chapman AR, Bularga A, Mills NL", "date": "2020-04-07", "evidence": [], "reference": [ { "id": "32251612", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32251612" } ] }, { "title": "Biochemical biomarkers alterations in Coronavirus Disease 2019 (COVID-19).", "journal": "Diagnosis (Berlin, Germany)", "authors": "Ciaccio M, Agnello L", "date": "2020-06-27", "evidence": [], "reference": [ { "id": "32589600", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32589600" } ] }, { "title": "Changes of Laboratory Cardiac Markers and Mechanisms of Cardiac Injury in Coronavirus Disease 2019.", "journal": "BioMed research international", "authors": "Li L, Zhou Q, Xu J", "date": "2020-07-01", "evidence": [], "reference": [ { "id": "32596365", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32596365" } ] }, { "title": "The clinical characteristics of myocardial injury in severe and very severe patients with 2019 novel coronavirus disease.", "journal": "The Journal of infection", "authors": "Zhou B, She J, Wang Y, Ma X", "date": "2020-03-27", "evidence": [], "reference": [ { "id": "32209382", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32209382" } ] } ], "biomarker_canonical_id": "AN6749", "score": 3.4, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 7 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "c": "condition", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6750-1", "biomarker_component": [ { "biomarker": "decreased K+ level", "assessed_biomarker_entity": { "recommended_name": "Potassium", "synonyms": [] }, "assessed_biomarker_entity_id": "PCCID:5462222", "assessed_entity_type": "chemical element", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "51720-1" } ], "evidence_source": [ { "id": "25325058", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/25325058", "evidence_list": [ { "evidence": "Diabetic patients frequently develop a constellation of electrolyte disorders. These disturbances are particularly common in decompensated diabetics, especially in the context of diabetic ketoacidosis or nonketotic hyperglycemic hyperosmolar syndrome. These patients are markedly potassium, magnesium and phosphate-depleted." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] }, { "biomarker": "Decreased K level", "assessed_biomarker_entity": { "recommended_name": "Potassium", "synonyms": [] }, "assessed_biomarker_entity_id": "PCCID:5462222", "assessed_entity_type": "chemical element", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "2947-0" } ], "evidence_source": [ { "id": "18488152", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/18488152", "evidence_list": [ { "evidence": "The results of this study showed that the mean values of K, Mg, and Ca were significantly reduced, while Na level were higher in blood and scalp hair samples of hypertensive diabetic (HD) patients and nonhypertensive diabetic (NHD) patients as compared to control subjects of both genders (p < 0.05), but level of K in the biological samples of nonhypertensive diabetic patient was found to be higher, but it was not significant (p = 0.05)." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:9351", "recommended_name": { "id": "DOID:9351", "name": "diabetes mellitus", "description": "A glucose metabolism disease that is characterized by chronic hyperglycaemia with disturbances of carbohydrate, fat and protein metabolism resulting from defects in insulin secretion, insulin action, or both.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_9351" }, "synonyms": [ { "id": "DOID:9351", "name": "diabetes", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_9351" } ] }, "evidence_source": [ { "id": "25325058", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/25325058", "evidence_list": [ { "evidence": "Diabetic patients frequently develop a constellation of electrolyte disorders. These disturbances are particularly common in decompensated diabetics, especially in the context of diabetic ketoacidosis or nonketotic hyperglycemic hyperosmolar syndrome. These patients are markedly potassium, magnesium and phosphate-depleted." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "18488152", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/18488152", "evidence_list": [ { "evidence": "The results of this study showed that the mean values of K, Mg, and Ca were significantly reduced, while Na level were higher in blood and scalp hair samples of hypertensive diabetic (HD) patients and nonhypertensive diabetic (NHD) patients as compared to control subjects of both genders (p < 0.05), but level of K in the biological samples of nonhypertensive diabetic patient was found to be higher, but it was not significant (p = 0.05)." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Diabetes mellitus and electrolyte disorders.", "journal": "World journal of clinical cases", "authors": "Liamis G, Liberopoulos E, Barkas F, Elisaf M", "date": "2014-10-18", "evidence": [], "reference": [ { "id": "25325058", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/25325058" } ] }, { "title": "Potassium, calcium, magnesium, and sodium levels in biological samples of hypertensive and nonhypertensive diabetes mellitus patients.", "journal": "Biological trace element research", "authors": "Afridi HI, Kazi TG, Kazi N, Jamali MK, Arain MB, Jalbani N, Sarfaraz RA, Shah A, Kandhro GA, Shah AQ, Baig JA", "date": "2008-05-20", "evidence": [], "reference": [ { "id": "18488152", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/18488152" } ] } ], "biomarker_canonical_id": "AN6750", "score": 2.2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 1 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "f": "frequency", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6375-1", "biomarker_component": [ { "biomarker": "decreased SERPINC1 level", "assessed_biomarker_entity": { "recommended_name": "Antithrombin", "synonyms": [ { "synonym": "ATIII" }, { "synonym": "Serpin C1" } ] }, "assessed_biomarker_entity_id": "UPKB:P01008", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "20991-6" } ], "evidence_source": [ { "id": "32172226", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32172226", "evidence_list": [ { "evidence": "Compared with healthy controls, the AT values were found to be lower in COVID-19 patients (85% vs. 99%; p<0.001)." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32829961", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32829961", "evidence_list": [ { "evidence": "The correlation between AT reduction to clinical outcomes can be extrapolated from studies in sepsis where this association has already been well established." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:0080600", "recommended_name": { "id": "DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, "synonyms": [ { "id": "DOID:0080600", "name": "SARS-CoV-2 infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan coronavirus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "COVID19", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan seafood market pneumonia virus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019-nCoV infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019 Novel Coronavirus (2019-nCoV)", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" } ] }, "evidence_source": [ { "id": "32172226", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32172226", "evidence_list": [ { "evidence": "Compared with healthy controls, the AT values were found to be lower in COVID-19 patients (85% vs. 99%; p<0.001)." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32829961", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32829961", "evidence_list": [ { "evidence": "The correlation between AT reduction to clinical outcomes can be extrapolated from studies in sepsis where this association has already been well established." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Prominent changes in blood coagulation of patients with SARS-CoV-2 infection.", "journal": "Clinical chemistry and laboratory medicine", "authors": "Han H, Yang L, Liu R, Liu F, Wu KL, Li J, Liu XH, Zhu CL", "date": "2020-03-17", "evidence": [], "reference": [ { "id": "32172226", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32172226" } ] }, { "title": "Understanding the andromeda strain - The role of cytokine release, coagulopathy and antithrombin III in SARS-CoV2 critical illness.", "journal": "Blood reviews", "authors": "Mir N, D'Amico A, Dasher J, Tolwani A, Valentine V", "date": "2020-08-25", "evidence": [], "reference": [ { "id": "32829961", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32829961" } ] } ], "biomarker_canonical_id": "AN6375", "score": 2.2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 1 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "f": "frequency", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6376-1", "biomarker_component": [ { "biomarker": "increased SERPINC1 level", "assessed_biomarker_entity": { "recommended_name": "Antithrombin", "synonyms": [ { "synonym": "ATIII" }, { "synonym": "Serpin C1" } ] }, "assessed_biomarker_entity_id": "UPKB:P01008", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "20991-6" } ], "evidence_source": [ { "id": "19227008", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/19227008", "evidence_list": [ { "evidence": "Our results pointed antithrombin (down) and fibrinogen (up) regulated after a four months treatment deserving to be further verified as prognostic markers for this treatment. Possible links between tumor progression and anti-thrombin expression level are also discussed." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1319" }, "synonyms": [ { "id": "DOID:1319", "name": "malignant brain tumour", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1319" }, { "id": "DOID:1319", "name": "BT - Brain tumour", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1319" }, { "id": "DOID:1319", "name": "neoplasm of brain", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1319" }, { "id": "DOID:1319", "name": "malignant primary brain tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1319" }, { "id": "DOID:1319", "name": "adult malignant brain neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1319" }, { "id": "DOID:1319", "name": "brain neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1319" }, { "id": "DOID:1319", "name": "malignant primary brain neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1319" }, { "id": "DOID:1319", "name": "primary malignant neoplasm of brain", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1319" }, { "id": "DOID:1319", "name": "adult brain tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1319" }, { "id": "DOID:1319", "name": "malignant tumor of Brain", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1319" }, { "id": "DOID:1319", "name": "malignant tumor of adult brain", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1319" }, { "id": "DOID:1319", "name": "primary brain tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1319" }, { "id": "DOID:1319", "name": "tumor of the Brain", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1319" }, { "id": "DOID:1319", "name": "primary brain neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1319" }, { "id": "DOID:1319", "name": "brain neoplasm, adult", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1319" } ] }, "evidence_source": [ { "id": "19227008", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/19227008", "evidence_list": [ { "evidence": "Our results pointed antithrombin (down) and fibrinogen (up) regulated after a four months treatment deserving to be further verified as prognostic markers for this treatment. Possible links between tumor progression and anti-thrombin expression level are also discussed." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Anti-thrombin as a prognostic biomarker candidate for patients with recurrent glioblastoma multiform under treatment with perillyl alcohol.", "journal": "Journal of experimental therapeutics & oncology", "authors": "Fischer Jde S, Carvalho PC, Neves-Ferreira AG, da Fonseca CO, Perales J, Carvalho Mda G, Domont GB", "date": "2009-02-21", "evidence": [], "reference": [ { "id": "19227008", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/19227008" } ] } ], "biomarker_canonical_id": "AN6376", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "f": "frequency", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6377-1", "biomarker_component": [ { "biomarker": "increased FIB level", "assessed_biomarker_entity": { "recommended_name": "Fibrinogen", "synonyms": [] }, "assessed_biomarker_entity_id": "UPKB:P02671", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "30009-5" } ], "evidence_source": [ { "id": "32172226", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32172226", "evidence_list": [ { "evidence": "FIB values in SARS-CoV-2 patients were also higher than those in the control group (5.02 vs. 2.90 g/L; p<0.001)." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32367765", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32367765", "evidence_list": [ { "evidence": "Fibrinogen levels were shown to be much higher in patients with severe COVID-19 patients." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:0080600", "recommended_name": { "id": "DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, "synonyms": [ { "id": "DOID:0080600", "name": "SARS-CoV-2 infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan coronavirus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "COVID19", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan seafood market pneumonia virus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019-nCoV infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019 Novel Coronavirus (2019-nCoV)", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" } ] }, "evidence_source": [ { "id": "32172226", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32172226", "evidence_list": [ { "evidence": "FIB values in SARS-CoV-2 patients were also higher than those in the control group (5.02 vs. 2.90 g/L; p<0.001)." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32367765", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32367765", "evidence_list": [ { "evidence": "Fibrinogen levels were shown to be much higher in patients with severe COVID-19 patients." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Prominent changes in blood coagulation of patients with SARS-CoV-2 infection.", "journal": "Clinical chemistry and laboratory medicine", "authors": "Han H, Yang L, Liu R, Liu F, Wu KL, Li J, Liu XH, Zhu CL", "date": "2020-03-17", "evidence": [], "reference": [ { "id": "32172226", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32172226" } ] }, { "title": "Prediction of severe illness due to COVID-19 based on an analysis of initial Fibrinogen to Albumin Ratio and Platelet count.", "journal": "Platelets", "authors": "Bi X, Su Z, Yan H, Du J, Wang J, Chen L, Peng M, Chen S, Shen B, Li J", "date": "2020-05-06", "evidence": [], "reference": [ { "id": "32367765", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32367765" } ] } ], "biomarker_canonical_id": "AN6377", "score": 2.2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 1 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "c": "condition", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6378-1", "biomarker_component": [ { "biomarker": "increased NET level", "assessed_biomarker_entity": { "recommended_name": "Neutrophil extracellular trap", "synonyms": [] }, "assessed_biomarker_entity_id": "NCIt:C180931", "assessed_entity_type": "DNA", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "32329756", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32329756", "evidence_list": [ { "evidence": "We now report that sera from patients with COVID-19 (n=50 patients, n=84 samples) have elevated levels of cell-free DNA, myeloperoxidase (MPO)-DNA, and citrullinated histone H3 (Cit-H3); 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In summary, these data reveal high levels of NETs in many patients with COVID-19, where they may contribute to cytokine release and respiratory failure." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32302401", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32302401", "evidence_list": [ { "evidence": "Indeed, we posit here that excess NETs may elicit the severe multi-organ consequences of COVID-19 via their known effects on tissues and the immune, vascular, and coagulation systems. 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There are multiple individual or combinatorial - and likely safe - therapeutic strategies available to antagonize NETs in COVID-19 patients today, and NETs themselves may be an appropriate biomarker to follow studies to test their efficacy." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "2329756", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/2329756", "evidence_list": [ { "evidence": "In summary, these data reveal high levels of NETs in many patients with COVID-19, where they may contribute to cytokine release and respiratory failure." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Neutrophil extracellular traps in COVID-19.", "journal": "JCI insight", "authors": "Zuo Y, Yalavarthi S, Shi H, Gockman K, Zuo M, Madison JA, Blair C, Weber A, Barnes BJ, Egeblad M, Woods RJ, Kanthi Y, Knight JS", "date": "2020-04-25", "evidence": [], "reference": [ { "id": "32329756", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32329756" } ] }, { "title": "Targeting potential drivers of COVID-19: Neutrophil extracellular traps.", "journal": "The Journal of experimental medicine", "authors": "Barnes BJ, Adrover JM, Baxter-Stoltzfus A, Borczuk A, Cools-Lartigue J, Crawford JM, Daßler-Plenker J, Guerci P, Huynh C, Knight JS, Loda M, Looney MR, McAllister F, Rayes R, Renaud S, Rousseau S, Salvatore S, Schwartz RE, Spicer JD, Yost CC, Weber A, Zuo Y, Egeblad M", "date": "2020-04-18", "evidence": [], "reference": [ { "id": "32302401", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32302401" } ] }, { "title": "[Amebic liver abscess treated by percutaneous drainage].", "journal": "Khirurgiia", "authors": "Samoĭlenko GA, Olenich VP, Chepkunov EF", "date": "1990-01-01", "evidence": [], "reference": [ { "id": "2329756", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/2329756" } ] } ], "biomarker_canonical_id": "AN6378", "score": 1.4, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 2 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "c": "condition", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6378-2", "biomarker_component": [ { "biomarker": "increased NET level", "assessed_biomarker_entity": { "recommended_name": "Neutrophil extracellular trap", "synonyms": [] }, "assessed_biomarker_entity_id": "NCIt:C180931", "assessed_entity_type": "DNA", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "30671057", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30671057", "evidence_list": [ { "evidence": "The results showed that NETs formation was obviously elevated in T2DM patients. An increased NETs formation was observed in DWR, NPDR, and PDR groups when compared with healthy controls. NE expression was also elevated in T2DM patients when compared with healthy controls." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:9351", "recommended_name": { "id": "DOID:9351", "name": "diabetes mellitus", "description": "A glucose metabolism disease that is characterized by chronic hyperglycaemia with disturbances of carbohydrate, fat and protein metabolism resulting from defects in insulin secretion, insulin action, or both.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_9351" }, "synonyms": [ { "id": "DOID:9351", "name": "diabetes", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_9351" } ] }, "evidence_source": [ { "id": "30671057", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30671057", "evidence_list": [ { "evidence": "The results showed that NETs formation was obviously elevated in T2DM patients. 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In summary, these data reveal high levels of NETs in many patients with COVID-19, where they may contribute to cytokine release and respiratory failure." } ], "tags": [ { "tag": "condition" }, { "tag": "best_biomarker_role" } ] } ], "citation": [ { "title": "Neutrophil extracellular traps in COVID-19.", "journal": "JCI insight", "authors": "Zuo Y, Yalavarthi S, Shi H, Gockman K, Zuo M, Madison JA, Blair C, Weber A, Barnes BJ, Egeblad M, Woods RJ, Kanthi Y, Knight JS", "date": "2020-04-25", "evidence": [], "reference": [ { "id": "32329756", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32329756" } ] } ], "biomarker_canonical_id": "AN6379", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "w": "weight", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6379-2", "biomarker_component": [ { "biomarker": "increased CIT-H3 level", "assessed_biomarker_entity": { "recommended_name": "Citrullinated histone H3", "synonyms": [ { "synonym": "Histone H3/a" }, { "synonym": "Histone H3/b" }, { "synonym": "Histone H3/c" }, { "synonym": "Histone H3/d" }, { "synonym": "Histone H3/f" }, { "synonym": "Histone H3/h" }, { "synonym": "Histone H3/i" }, { "synonym": "Histone H3/j" }, { "synonym": "Histone H3/k" }, { "synonym": "Histone H3/l" } ] }, "assessed_biomarker_entity_id": "UPKB:P68431", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "29324871", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/29324871", "evidence_list": [ { "evidence": "Our results are the first to unveil H3Cit as a potential diagnostic and prognostic blood marker associated with an exacerbated inflammatory response in patients with advanced cancer." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "name": "Advanced Cancer", "description": "A respiratory system cancer that is located_in the lung.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1324" }, "synonyms": [] }, "evidence_source": [ { "id": "29324871", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/29324871", "evidence_list": [ { "evidence": "Our results are the first to unveil H3Cit as a potential diagnostic and prognostic blood marker associated with an exacerbated inflammatory response in patients with advanced cancer." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Citrullinated histone H3 as a novel prognostic blood marker in patients with advanced cancer.", "journal": "PloS one", "authors": "Thålin C, Lundström S, Seignez C, Daleskog M, Lundström A, Henriksson P, Helleday T, Phillipson M, Wallén H, Demers M", "date": "2018-01-13", "evidence": [], "reference": [ { "id": "29324871", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/29324871" } ] } ], "biomarker_canonical_id": "AN6379", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "w": "weight", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6380-1", "biomarker_component": [ { "biomarker": "increased cfDNA level", "assessed_biomarker_entity": { "recommended_name": "Cell-free DNA", "synonyms": [] }, "assessed_biomarker_entity_id": "NCIt:C128274", "assessed_entity_type": "DNA", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "30992036", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30992036", "evidence_list": [ { "evidence": "In T2DM, NETosis markers in circulating plasma, such as H3Cit and cfDNA, are related to glycemia control, systemic low-grade inflammation markers and previous MI. 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Most liver diseases initially cause mild symptoms, but they must be detected early." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32438331", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32438331", "evidence_list": [ { "evidence": "Liver dysfunction with chronically increased serum Alanine aminotransferase indicates adverse outcome of COVID-19." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32234718", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32234718", "evidence_list": [ { "evidence": "Increase in alanine aminotransferase can be used to predict COVID-19 severity." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32171076", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32171076", "evidence_list": [ { "evidence": "Age, comorbidities, lymphocytopenia and elevated alanine aminotransferase, d-dimer, creatine kinase, high-sensitivity cardiac troponin I, prothrombin time, and disease severity were reported to be associated with intensive care unit admission." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32259132", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32259132", "evidence_list": [ { "evidence": "Our findings suggest that level of LDH, CRP, ALT and NEU can be used to predict the result of COVID-19 test." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32589600", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32589600", "evidence_list": [ { "evidence": "Many biomarkers have been associated with poor outcomes and represent a candidate for risk stratification models for predicting severe COVID-19 in order to guide clinical care. Among all, lymphopenia, thrombocytopenia, leucocytosis, CRP, PCT, LDH, AST, ALT, D-dimer, cTn represent the most predictive parameters of severe COVID-19" } ], "tags": [ { "tag": "condition" }, { "tag": "best_biomarker_role" } ] }, { "id": "20376881", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/20376881", "evidence_list": [ { "evidence": "Increased levels of AST had a higher risk for esophageal cancer." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "COVID-19 and the clinical hematology laboratory.", "journal": "International journal of laboratory hematology", "authors": "Frater JL, Zini G, d'Onofrio G, Rogers HJ", "date": "2020-04-21", "evidence": [], "reference": [ { "id": "32311826", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32311826" } ] }, { "title": "Alteration of Liver Biomarkers in Patients with SARS-CoV-2 (COVID-19).", "journal": "Journal of inflammation research", "authors": "Gholizadeh P, Safari R, Marofi P, Zeinalzadeh E, Pagliano P, Ganbarov K, Esposito S, Khodadadi E, Yousefi M, Samadi Kafil H", "date": "2020-07-17", "evidence": [], "reference": [ { "id": "32669866", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32669866" } ] }, { "title": "Diabetes and metabolic syndrome as risk factors for COVID-19.", "journal": "Diabetes & metabolic syndrome", "authors": "Marhl M, Grubelnik V, Magdič M, Markovič R", "date": "2020-05-22", "evidence": [], "reference": [ { "id": "32438331", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32438331" } ] }, { "title": "Clinical characteristics of 113 deceased patients with coronavirus disease 2019: retrospective study.", "journal": "BMJ (Clinical research ed.)", "authors": "", "date": "2020-04-03", "evidence": [], "reference": [ { "id": "32234718", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32234718" } ] }, { "title": "Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: a retrospective cohort study.", "journal": "Lancet (London, England)", "authors": "Zhou F, Yu T, Du R, Fan G, Liu Y, Liu Z, Xiang J, Wang Y, Song B, Gu X, Guan L, Wei Y, Li H, Wu X, Xu J, Tu S, Zhang Y, Chen H, Cao B", "date": "2020-03-15", "evidence": [], "reference": [ { "id": "32171076", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32171076" } ] }, { "title": "Laboratory Parameters in Detection of COVID-19 Patients with Positive RT-PCR; a Diagnostic Accuracy Study.", "journal": "Archives of academic emergency medicine", "authors": "Mardani R, Ahmadi Vasmehjani A, Zali F, Gholami A, Mousavi Nasab SD, Kaghazian H, Kaviani M, Ahmadi N", "date": "2020-04-08", "evidence": [], "reference": [ { "id": "32259132", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32259132" } ] }, { "title": "The independent effects of cigarette smoking, alcohol consumption, and serum aspartate aminotransferase on the alanine aminotransferase ratio in korean men for the risk for esophageal cancer.", "journal": "Yonsei medical journal", "authors": "Kimm H, Kim S, Jee SH", "date": "2010-04-09", "evidence": [], "reference": [ { "id": "20376881", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/20376881" } ] }, { "title": "Biochemical biomarkers alterations in Coronavirus Disease 2019 (COVID-19).", "journal": "Diagnosis (Berlin, Germany)", "authors": "Ciaccio M, Agnello L", "date": "2020-06-27", "evidence": [], "reference": [ { "id": "32589600", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32589600" } ] } ], "biomarker_canonical_id": "AN6384", "score": 3.4, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 7 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6383-1", "biomarker_component": [ { "biomarker": "increased GGT level", "assessed_biomarker_entity": { "recommended_name": "Gamma Glutamyltransferase", "synonyms": [ { "synonym": "Gamma-glutamyltransferase 1" }, { "synonym": "Gamma-glutamyltranspeptidase 1" }, { "synonym": "GGT 1" }, { "synonym": "Leukotriene-C4 hydrolase" } ] }, "assessed_biomarker_entity_id": "UPKB:P19440", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "76625-3" } ], "evidence_source": [ { "id": "25043373", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/25043373", "evidence_list": [ { "evidence": "Several prospective studies have demonstrated associations between GGT or ALT and risk of type 2 diabetes mellitus, cardiovascular disease, vascular and nonvascular mortality, and all cause mortality outcomes. 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{ "id": "DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "Ca middle third oesophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant neoplasm of upper third esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "esophagus cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" } ] }, "evidence_source": [ { "id": "20376881", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/20376881", "evidence_list": [ { "evidence": "Increased levels of AST had a higher risk for esophageal cancer." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "The independent effects of cigarette smoking, alcohol consumption, and serum aspartate aminotransferase on the alanine aminotransferase ratio in korean men for the risk for esophageal cancer.", "journal": "Yonsei medical journal", "authors": "Kimm H, Kim S, Jee SH", "date": "2010-04-09", "evidence": [], "reference": [ { "id": "20376881", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/20376881" } ] } ], "biomarker_canonical_id": "AN6751", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6387-1", "biomarker_component": [ { "biomarker": "Increased leukocyte level", "assessed_biomarker_entity": { "recommended_name": "Leucocytosis", "synonyms": [] }, "assessed_biomarker_entity_id": "NCIt:C12529", "assessed_entity_type": "cell", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "2157-6" } ], "evidence_source": [ { "id": "32589600", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32589600", "evidence_list": [ { "evidence": "Many biomarkers have been associated with poor outcomes and represent a candidate for risk stratification models for predicting severe COVID-19 in order to guide clinical care. Among all, lymphopenia, thrombocytopenia, leucocytosis, CRP, PCT, LDH, AST, ALT, D-dimer, cTn represent the most predictive parameters of severe COVID-19" } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:0080600", "recommended_name": { "id": "DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, "synonyms": [ { "id": "DOID:0080600", "name": "SARS-CoV-2 infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan coronavirus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "COVID19", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan seafood market pneumonia virus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019-nCoV infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019 Novel Coronavirus (2019-nCoV)", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" } ] }, "evidence_source": [ { "id": "32589600", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32589600", "evidence_list": [ { "evidence": "Many biomarkers have been associated with poor outcomes and represent a candidate for risk stratification models for predicting severe COVID-19 in order to guide clinical care. Among all, lymphopenia, thrombocytopenia, leucocytosis, CRP, PCT, LDH, AST, ALT, D-dimer, cTn represent the most predictive parameters of severe COVID-19" } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Biochemical biomarkers alterations in Coronavirus Disease 2019 (COVID-19).", "journal": "Diagnosis (Berlin, Germany)", "authors": "Ciaccio M, Agnello L", "date": "2020-06-27", "evidence": [], "reference": [ { "id": "32589600", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32589600" } ] } ], "biomarker_canonical_id": "AN6387", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "f": "frequency", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6752-1", "biomarker_component": [ { "biomarker": "increased CK level", "assessed_biomarker_entity": { "recommended_name": "Creatine kinase", "synonyms": [] }, "assessed_biomarker_entity_id": "PRO:PR_000050361", "assessed_entity_type": "protein complex", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "2157-6" } ], "evidence_source": [ { "id": "32589600", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32589600", "evidence_list": [ { "evidence": "COVID-19 patients typically present increased levels of biomarkers of muscle injury, namely creatine-kinase (CK) and myoglobin. However, the alterations of such biomarkers could be the result of several clinical conditions, including kidney dysfunction and cardiac injury, or a direct effect of the SARS-CoV-2, which can also infect cells of the muscle tissue due to the expression of the ACE2 receptor." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32503382", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32503382", "evidence_list": [ { "evidence": "To sum up, we can conclude from the analysis of published studies that hematological (lymphocyte count, neutrophil count, and NLR), inflammatory (CRP, ESR, IL-6), and especially biochemical (D-dimer, Troponins, CK) parameters correlate with severe prognosis or exitus in COVID-19 patients and can therefore be used as predictive biomarkers." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32247631", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32247631", "evidence_list": [ { "evidence": "In keeping with this observation, 138 patients with COVID-19, who were admitted to an intensive care unit, showed a tendency toward increased creatine kinase levels." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32171076", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32171076", "evidence_list": [ { "evidence": "Age, comorbidities, lymphocytopenia and elevated alanine aminotransferase, d-dimer, creatine kinase, high-sensitivity cardiac troponin I, prothrombin time, and disease severity were reported to be associated with intensive care unit admission." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:0080600", "recommended_name": { "id": "DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, "synonyms": [ { "id": "DOID:0080600", "name": "SARS-CoV-2 infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan coronavirus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "COVID19", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan seafood market pneumonia virus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019-nCoV infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019 Novel Coronavirus (2019-nCoV)", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" } ] }, "evidence_source": [ { "id": "32589600", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32589600", "evidence_list": [ { "evidence": "COVID-19 patients typically present increased levels of biomarkers of muscle injury, namely creatine-kinase (CK) and myoglobin. However, the alterations of such biomarkers could be the result of several clinical conditions, including kidney dysfunction and cardiac injury, or a direct effect of the SARS-CoV-2, which can also infect cells of the muscle tissue due to the expression of the ACE2 receptor." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32503382", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32503382", "evidence_list": [ { "evidence": "To sum up, we can conclude from the analysis of published studies that hematological (lymphocyte count, neutrophil count, and NLR), inflammatory (CRP, ESR, IL-6), and especially biochemical (D-dimer, Troponins, CK) parameters correlate with severe prognosis or exitus in COVID-19 patients and can therefore be used as predictive biomarkers." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32247631", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32247631", "evidence_list": [ { "evidence": "In keeping with this observation, 138 patients with COVID-19, who were admitted to an intensive care unit, showed a tendency toward increased creatine kinase levels." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32171076", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32171076", "evidence_list": [ { "evidence": "Age, comorbidities, lymphocytopenia and elevated alanine aminotransferase, d-dimer, creatine kinase, high-sensitivity cardiac troponin I, prothrombin time, and disease severity were reported to be associated with intensive care unit admission." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32596365", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32596365", "evidence_list": [ { "evidence": "The levels of laboratory cardiac markers, lactose dehydrogenase (LDH), creatine kinase (CK), creatinine kinase-muscle/brain activity (CK-MB), myoglobin (Mb), cardiac troponin I (cTnI), alpha-hydroxybutyrate dehydrogenase (α-HBDH), aspartate aminotransferase (AST), and N-terminal of the prohormone brain natriuretic peptide (NT-proBNP) increase in different proportions in patients with COVID-19 (see Table 1)." } ], "tags": [ { "tag": "condition" }, { "tag": "best_biomarker_role" } ] }, { "id": "32209382", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32209382", "evidence_list": [ { "evidence": "This study reveals that the heart is also a major target of COVID-19 infection, and myocardial enzyme spectrum assays could help the diagnosis, prognosis and guide the treatments to prevent heart failure in COVID-19 patients. [DOI:https://doi.org/10.21203/rs.3.rs-23849/v1] We noted significantly increased cTnI, CK, HBDB and LDH levels in very severe group as compare to severe." } ], "tags": [ { "tag": "condition" }, { "tag": "best_biomarker_role" } ] } ], "citation": [ { "title": "Biochemical biomarkers alterations in Coronavirus Disease 2019 (COVID-19).", "journal": "Diagnosis (Berlin, Germany)", "authors": "Ciaccio M, Agnello L", "date": "2020-06-27", "evidence": [], "reference": [ { "id": "32589600", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32589600" } ] }, { "title": "Biomarkers associated with COVID-19 disease progression.", "journal": "Critical reviews in clinical laboratory sciences", "authors": "Ponti G, Maccaferri M, Ruini C, Tomasi A, Ozben T", "date": "2020-06-07", "evidence": [], "reference": [ { "id": "32503382", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32503382" } ] }, { "title": "Kidney disease is associated with in-hospital death of patients with COVID-19.", "journal": "Kidney international", "authors": "Cheng Y, Luo R, Wang K, Zhang M, Wang Z, Dong L, Li J, Yao Y, Ge S, Xu G", "date": "2020-04-06", "evidence": [], "reference": [ { "id": "32247631", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32247631" } ] }, { "title": "Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: a retrospective cohort study.", "journal": "Lancet (London, England)", "authors": "Zhou F, Yu T, Du R, Fan G, Liu Y, Liu Z, Xiang J, Wang Y, Song B, Gu X, Guan L, Wei Y, Li H, Wu X, Xu J, Tu S, Zhang Y, Chen H, Cao B", "date": "2020-03-15", "evidence": [], "reference": [ { "id": "32171076", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32171076" } ] }, { "title": "Changes of Laboratory Cardiac Markers and Mechanisms of Cardiac Injury in Coronavirus Disease 2019.", "journal": "BioMed research international", "authors": "Li L, Zhou Q, Xu J", "date": "2020-07-01", "evidence": [], "reference": [ { "id": "32596365", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32596365" } ] }, { "title": "The clinical characteristics of myocardial injury in severe and very severe patients with 2019 novel coronavirus disease.", "journal": "The Journal of infection", "authors": "Zhou B, She J, Wang Y, Ma X", "date": "2020-03-27", "evidence": [], "reference": [ { "id": "32209382", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32209382" } ] } ], "biomarker_canonical_id": "AN6752", "score": 3, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 5 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6390-1", "biomarker_component": [ { "biomarker": "decreased Na+ level", "assessed_biomarker_entity": { "recommended_name": "Sodium", "synonyms": [] }, "assessed_biomarker_entity_id": "PCCID:5360545", "assessed_entity_type": "chemical element", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "33552948", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/33552948", "evidence_list": [ { "evidence": "Lower levels of sodium can indicate poorer results of esophageal carcinoma, but higher survival benefits of adjuvant therapy." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus.", "resource": "Disease 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It could also participate in the significant weight loss that is observed in patients with COVID-19." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Patients with COVID-19 present with low plasma citrulline concentrations that associate with systemic inflammation and gastrointestinal symptoms.", "journal": "Digestive and liver disease : official journal of the Italian Society of Gastroenterology and the Italian Association for the Study of the Liver", "authors": "Uzzan M, Soudan D, Peoc'h K, Weiss E, Corcos O, Treton X", "date": "2020-07-11", "evidence": [], "reference": [ { "id": "32646736", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32646736" } ] } ], "biomarker_canonical_id": "AN6395", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "c": "condition", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6395-2", "biomarker_component": [ { "biomarker": "decreased CIT level", "assessed_biomarker_entity": { "recommended_name": "Plasma citrulline", "synonyms": [ { "synonym": "Cit" }, { "synonym": "N(5)-(aminocarbonyl)-DL-ornithine" }, { "synonym": "N(5)-(aminocarbonyl)ornithine" }, { "synonym": "2-amino-5-(carbamoylamino)pentanoic acid" }, { "synonym": "N(5)-carbamoyl-DL-ornithine" }, { "synonym": "N(5)-carbamoylornithine" }, { "synonym": "citrulina" }, { "synonym": "Citrullin" }, { "synonym": "DL-2-amino-5-ureidovaleric acid" }, { "synonym": "dl-citrulline" }, { "synonym": "citrulline" }, { "synonym": "Citrulline" }, { "synonym": "2-Amino-5-uredovaleric acid" } ] }, "assessed_biomarker_entity_id": "CHEBI:18211", "assessed_entity_type": "metabolite", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "2129-5" } ], "evidence_source": [ { "id": "25473654", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/25473654", "evidence_list": [ { "evidence": "Plasma citrulline (Cit) is an amino acid that is produced by small bowel enterocytes. The plasma citrulline level is a reliable and objective biochemical marker of enterocyte mass and function in humans, and therefore can be used to monitor enterocyte toxicity resulting from chemotherapy and radiotherapy during anticancer therapy in patients with severely disturbed gut integrity." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_9256" }, "synonyms": [] }, "evidence_source": [ { "id": "25473654", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/25473654", "evidence_list": [ { "evidence": "Plasma citrulline (Cit) is an amino acid that is produced by small bowel enterocytes. The plasma citrulline level is a reliable and objective biochemical marker of enterocyte mass and function in humans, and therefore can be used to monitor enterocyte toxicity resulting from chemotherapy and radiotherapy during anticancer therapy in patients with severely disturbed gut integrity." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Plasma citrulline level as a biomarker for cancer therapy-induced small bowel mucosal damage.", "journal": "Acta biochimica Polonica", "authors": "Barzał JA, Szczylik C, Rzepecki P, Jaworska M, Anuszewska E", "date": "2014-12-05", "evidence": [], "reference": [ { "id": "25473654", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/25473654" } ] } ], "biomarker_canonical_id": "AN6395", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "c": "condition", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6753-1", "biomarker_component": [ { "biomarker": "increased CK-MB level", "assessed_biomarker_entity": { "recommended_name": "Creatine kinase MB", "synonyms": [] }, "assessed_biomarker_entity_id": "PRO:PR_000050356", "assessed_entity_type": "protein complex", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "20569-0" } ], "evidence_source": [ { "id": "32220650", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32220650", "evidence_list": [ { "evidence": "Besides radiographic presentations, variables that were associated significantly with severity of COVID-19 were decreased lymphocytes, elevated body temperature, and high levels of procalcitonin, D-dimer, and creatine kinase MB." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32596365", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32596365", "evidence_list": [ { "evidence": "A meta-analysis which included 4189 confirmed patients of COVID-19 from 28 studies pointed out that cardiac injury biomarkers rose above normal by the midpoint of hospitalization and spiked immediately before death, which seemed to be the most seen in severe cases." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "monitoring" } ], "condition": { "id": "DOID:0080600", "recommended_name": { "id": "DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, "synonyms": [ { "id": "DOID:0080600", "name": "SARS-CoV-2 infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan coronavirus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "COVID19", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan seafood market pneumonia virus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019-nCoV infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019 Novel Coronavirus (2019-nCoV)", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" } ] }, "evidence_source": [ { "id": "32220650", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32220650", "evidence_list": [ { "evidence": "Besides radiographic presentations, variables that were associated significantly with severity of COVID-19 were decreased lymphocytes, elevated body temperature, and high levels of procalcitonin, D-dimer, and creatine kinase MB." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32596365", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32596365", "evidence_list": [ { "evidence": "A meta-analysis which included 4189 confirmed patients of COVID-19 from 28 studies pointed out that cardiac injury biomarkers rose above normal by the midpoint of hospitalization and spiked immediately before death, which seemed to be the most seen in severe cases." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32305557", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32305557", "evidence_list": [ { "evidence": "More severe COVID-19 infection is associated with higher mean troponin (SMD 0.53, 95% CI 0.30 to 0.75, p < 0.001), with a similar trend for creatine kinase-MB, myoglobin, and NT-proBNP." } ], "tags": [ { "tag": "condition" }, { "tag": "best_biomarker_role" } ] } ], "citation": [ { "title": "Clinical and epidemiological features of 36 children with coronavirus disease 2019 (COVID-19) in Zhejiang, China: an observational cohort study.", "journal": "The Lancet. Infectious diseases", "authors": "Qiu H, Wu J, Hong L, Luo Y, Song Q, Chen D", "date": "2020-03-30", "evidence": [], "reference": [ { "id": "32220650", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32220650" } ] }, { "title": "Changes of Laboratory Cardiac Markers and Mechanisms of Cardiac Injury in Coronavirus Disease 2019.", "journal": "BioMed research international", "authors": "Li L, Zhou Q, Xu J", "date": "2020-07-01", "evidence": [], "reference": [ { "id": "32596365", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32596365" } ] }, { "title": "The impact of 2019 novel coronavirus on heart injury: A Systematic review and Meta-analysis.", "journal": "Progress in cardiovascular diseases", "authors": "Li JW, Han TW, Woodward M, Anderson CS, Zhou H, Chen YD, Neal B", "date": "2020-04-20", "evidence": [], "reference": [ { "id": "32305557", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32305557" } ] } ], "biomarker_canonical_id": "AN6753", "score": 2.4, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 2 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "f": "frequency", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6754-1", "biomarker_component": [ { "biomarker": "Increased MB levels", "assessed_biomarker_entity": { "recommended_name": "Myoglobin", "synonyms": [] }, "assessed_biomarker_entity_id": "UPKB:P02144", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "20569-0" } ], "evidence_source": [ { "id": "32596365", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32596365", "evidence_list": [ { "evidence": "The levels of laboratory cardiac markers, lactose dehydrogenase (LDH), creatine kinase (CK), creatinine kinase-muscle/brain activity (CK-MB), myoglobin (Mb), cardiac troponin I (cTnI), alpha-hydroxybutyrate dehydrogenase (α-HBDH), aspartate aminotransferase (AST), and N-terminal of the prohormone brain natriuretic peptide (NT-proBNP) increase in different proportions in patients with COVID-19 (see Table 1)." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] }, { "biomarker": "increased MB level", "assessed_biomarker_entity": { "recommended_name": "Myoglobin", "synonyms": [] }, "assessed_biomarker_entity_id": "UPKB:P02144", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "2639-3" } ], "evidence_source": [ { "id": "32450473", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32450473", "evidence_list": [ { "evidence": "An increased concentration of myoglobin was associated with an increased risk of hospitalization mortality in non-survivors with NCIP. In conclusion, our study provides important documentation that in this single-center, an elevated serum concentration of myoglobin (>/=306.5 ug/L) is associated with an increased risk of hospitalization mortality in non-survivor with NCIP, independent of elevation in CK-MB and Troponin I levels." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32305557", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32305557", "evidence_list": [ { "evidence": "The severity of COVID-19 is associated with acute cardiac injury, and acute cardiac injury is associated with death. Cardiac injury biomarkers mainly increase in non-survivors. This highlights the need to effectively monitor heart health to prevent myocarditis in patients infected with COVID-19." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "monitoring" } ], "condition": { "id": "DOID:0080600", "recommended_name": { "id": "DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, "synonyms": [ { "id": "DOID:0080600", "name": "SARS-CoV-2 infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan coronavirus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "COVID19", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan seafood market pneumonia virus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019-nCoV infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019 Novel Coronavirus (2019-nCoV)", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" } ] }, "evidence_source": [ { "id": "32596365", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32596365", "evidence_list": [ { "evidence": "The levels of laboratory cardiac markers, lactose dehydrogenase (LDH), creatine kinase (CK), creatinine kinase-muscle/brain activity (CK-MB), myoglobin (Mb), cardiac troponin I (cTnI), alpha-hydroxybutyrate dehydrogenase (α-HBDH), aspartate aminotransferase (AST), and N-terminal of the prohormone brain natriuretic peptide (NT-proBNP) increase in different proportions in patients with COVID-19 (see Table 1)." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32450473", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32450473", "evidence_list": [ { "evidence": "An increased concentration of myoglobin was associated with an increased risk of hospitalization mortality in non-survivors with NCIP. In conclusion, our study provides important documentation that in this single-center, an elevated serum concentration of myoglobin (>/=306.5 ug/L) is associated with an increased risk of hospitalization mortality in non-survivor with NCIP, independent of elevation in CK-MB and Troponin I levels." } ], "tags": [ { "tag": "condition" }, { "tag": "best_biomarker_role" } ] }, { "id": "32305557", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32305557", "evidence_list": [ { "evidence": "The severity of COVID-19 is associated with acute cardiac injury, and acute cardiac injury is associated with death. Cardiac injury biomarkers mainly increase in non-survivors. This highlights the need to effectively monitor heart health to prevent myocarditis in patients infected with COVID-19." } ], "tags": [ { "tag": "condition" }, { "tag": "best_biomarker_role" } ] } ], "citation": [ { "title": "Changes of Laboratory Cardiac Markers and Mechanisms of Cardiac Injury in Coronavirus Disease 2019.", "journal": "BioMed research international", "authors": "Li L, Zhou Q, Xu J", "date": "2020-07-01", "evidence": [], "reference": [ { "id": "32596365", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32596365" } ] }, { "title": "Elevated cardiac biomarkers are associated with increased mortality for inpatients with COVID-19: A retrospective case-control study.", "journal": "Journal of clinical anesthesia", "authors": "Su M, Wang Y, Peng J, Wu MJ, Deng W, Yang YS", "date": "2020-05-26", "evidence": [], "reference": [ { "id": "32450473", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32450473" } ] }, { "title": "The impact of 2019 novel coronavirus on heart injury: A Systematic review and Meta-analysis.", "journal": "Progress in cardiovascular diseases", "authors": "Li JW, Han TW, Woodward M, Anderson CS, Zhou H, Chen YD, Neal B", "date": "2020-04-20", "evidence": [], "reference": [ { "id": "32305557", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32305557" } ] } ], "biomarker_canonical_id": "AN6754", "score": 2.4, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 2 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6401-1", "biomarker_component": [ { "biomarker": "increased ALDH5A1 level", "assessed_biomarker_entity": { "recommended_name": "Alpha-hydroxybutyric dehydrogenase", "synonyms": [ { "synonym": "Aldehyde dehydrogenase family 5 member A1" }, { "synonym": "NAD(+)-dependent succinic semialdehyde dehydrogenase" } ] }, "assessed_biomarker_entity_id": "UPKB:P51649", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "1677-4" } ], "evidence_source": [ { "id": "32596365", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32596365", "evidence_list": [ { "evidence": "The levels of laboratory cardiac markers, lactose dehydrogenase (LDH), creatine kinase (CK), creatinine kinase-muscle/brain activity (CK-MB), myoglobin (Mb), cardiac troponin I (cTnI), alpha-hydroxybutyrate dehydrogenase (α-HBDH), aspartate aminotransferase (AST), and N-terminal of the prohormone brain natriuretic peptide (NT-proBNP) increase in different proportions in patients with COVID-19 (see Table 1)." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32161968", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32161968", "evidence_list": [ { "evidence": "LDH and alpha-HBDH may be considerable markers for evaluation of NCOVID-19." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32209382", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32209382", "evidence_list": [ { "evidence": "This study reveals that the heart is also a major target of COVID-19 infection, and myocardial enzyme spectrum assays could help the diagnosis, prognosis and guide the treatments to prevent heart failure in COVID-19 patients. [DOI:https://doi.org/10.21203/rs.3.rs-23849/v1] We noted significantly increased cTnI, CK, HBDB and LDH levels in very severe group as compare to severe." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "monitoring" } ], "condition": { "id": "DOID:0080600", "recommended_name": { "id": "DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, "synonyms": [ { "id": "DOID:0080600", "name": "SARS-CoV-2 infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan coronavirus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "COVID19", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan seafood market pneumonia virus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019-nCoV infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019 Novel Coronavirus (2019-nCoV)", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" } ] }, "evidence_source": [ { "id": "32596365", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32596365", "evidence_list": [ { "evidence": "The levels of laboratory cardiac markers, lactose dehydrogenase (LDH), creatine kinase (CK), creatinine kinase-muscle/brain activity (CK-MB), myoglobin (Mb), cardiac troponin I (cTnI), alpha-hydroxybutyrate dehydrogenase (α-HBDH), aspartate aminotransferase (AST), and N-terminal of the prohormone brain natriuretic peptide (NT-proBNP) increase in different proportions in patients with COVID-19 (see Table 1)." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32209382", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32209382", "evidence_list": [ { "evidence": "This study reveals that the heart is also a major target of COVID-19 infection, and myocardial enzyme spectrum assays could help the diagnosis, prognosis and guide the treatments to prevent heart failure in COVID-19 patients. [DOI:https://doi.org/10.21203/rs.3.rs-23849/v1] We noted significantly increased cTnI, CK, HBDB and LDH levels in very severe group as compare to severe." } ], "tags": [ { "tag": "condition" }, { "tag": "best_biomarker_role" } ] }, { "id": "32161968", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32161968", "evidence_list": [ { "evidence": "LDH and alpha-HBDH may be considerable markers for evaluation of NCOVID-19." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Changes of Laboratory Cardiac Markers and Mechanisms of Cardiac Injury in Coronavirus Disease 2019.", "journal": "BioMed research international", "authors": "Li L, Zhou Q, Xu J", "date": "2020-07-01", "evidence": [], "reference": [ { "id": "32596365", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32596365" } ] }, { "title": "A Comparative Study on the Clinical Features of Coronavirus 2019 (COVID-19) Pneumonia With Other Pneumonias.", "journal": "Clinical infectious diseases : an official publication of the Infectious Diseases Society of America", "authors": "Zhao D, Yao F, Wang L, Zheng L, Gao Y, Ye J, Guo F, Zhao H, Gao R", "date": "2020-03-13", "evidence": [], "reference": [ { "id": "32161968", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32161968" } ] }, { "title": "The clinical characteristics of myocardial injury in severe and very severe patients with 2019 novel coronavirus disease.", "journal": "The Journal of infection", "authors": "Zhou B, She J, Wang Y, Ma X", "date": "2020-03-27", "evidence": [], "reference": [ { "id": "32209382", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32209382" } ] } ], "biomarker_canonical_id": "AN6401", "score": 2.4, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 2 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "f": "frequency", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6755-1", "biomarker_component": [ { "biomarker": "elevated HBDB level", "assessed_biomarker_entity": { "recommended_name": "α-Hydroxybutyrate Dehydrogenase", "synonyms": [ { "synonym": "LDH-B" }, { "synonym": "LDH heart subunit" }, { "synonym": "LDH-H" }, { "synonym": "Renal carcinoma antigen NY-REN-46" } ] }, "assessed_biomarker_entity_id": "UPKB:P07195", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "1677-4" } ], "evidence_source": [ { "id": "32209382", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32209382", "evidence_list": [ { "evidence": "This study reveals that the heart is also a major target of COVID-19 infection, and myocardial enzyme spectrum assays could help the diagnosis, prognosis and guide the treatments to prevent heart failure in COVID-19 patients. [DOI:https://doi.org/10.21203/rs.3.rs-23849/v1] We noted significantly increased cTnI, CK, HBDB and LDH levels in very severe group as compare to severe." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "monitoring" } ], "condition": { "id": "DOID:0080600", "recommended_name": { "id": "DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, "synonyms": [ { "id": "DOID:0080600", "name": "SARS-CoV-2 infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan coronavirus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "COVID19", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan seafood market pneumonia virus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019-nCoV infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019 Novel Coronavirus (2019-nCoV)", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" } ] }, "evidence_source": [ { "id": "32209382", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32209382", "evidence_list": [ { "evidence": "This study reveals that the heart is also a major target of COVID-19 infection, and myocardial enzyme spectrum assays could help the diagnosis, prognosis and guide the treatments to prevent heart failure in COVID-19 patients. [DOI:https://doi.org/10.21203/rs.3.rs-23849/v1] We noted significantly increased cTnI, CK, HBDB and LDH levels in very severe group as compare to severe." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32596365", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32596365", "evidence_list": [ { "evidence": "The levels of laboratory cardiac markers, lactose dehydrogenase (LDH), creatine kinase (CK), creatinine kinase-muscle/brain activity (CK-MB), myoglobin (Mb), cardiac troponin I (cTnI), alpha-hydroxybutyrate dehydrogenase (α-HBDH), aspartate aminotransferase (AST), and N-terminal of the prohormone brain natriuretic peptide (NT-proBNP) increase in different proportions in patients with COVID-19 (see Table 1)." } ], "tags": [ { "tag": "condition" }, { "tag": "best_biomarker_role" } ] } ], "citation": [ { "title": "The clinical characteristics of myocardial injury in severe and very severe patients with 2019 novel coronavirus disease.", "journal": "The Journal of infection", "authors": "Zhou B, She J, Wang Y, Ma X", "date": "2020-03-27", "evidence": [], "reference": [ { "id": "32209382", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32209382" } ] }, { "title": "Changes of Laboratory Cardiac Markers and Mechanisms of Cardiac Injury in Coronavirus Disease 2019.", "journal": "BioMed research international", "authors": "Li L, Zhou Q, Xu J", "date": "2020-07-01", "evidence": [], "reference": [ { "id": "32596365", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32596365" } ] } ], "biomarker_canonical_id": "AN6755", "score": 2.2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 1 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "c": "condition", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6400-1", "biomarker_component": [ { "biomarker": "increased NT-proBNP level", "assessed_biomarker_entity": { "recommended_name": "N-terminal of the Prohormone Brain Natriuretic Peptide", "synonyms": [ { "synonym": "Atrial natriuretic factor prohormone" }, { "synonym": "proANF" }, { "synonym": "Atrial natriuretic peptide prohormone" }, { "synonym": "preproANP" }, { "synonym": "proANP" }, { "synonym": "Atriopeptigen" }, { "synonym": "Cardiodilatin" }, { "synonym": "CDD" }, { "synonym": "preproCDD-ANF" } ] }, "assessed_biomarker_entity_id": "UPKB:P01160", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "20569-0" } ], "evidence_source": [ { "id": "32596365", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32596365", "evidence_list": [ { "evidence": "The levels of laboratory cardiac markers, lactose 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in non-survivors." } ], "tags": [ { "tag": "condition" }, { "tag": "best_biomarker_role" } ] } ], "citation": [ { "title": "Changes of Laboratory Cardiac Markers and Mechanisms of Cardiac Injury in Coronavirus Disease 2019.", "journal": "BioMed research international", "authors": "Li L, Zhou Q, Xu J", "date": "2020-07-01", "evidence": [], "reference": [ { "id": "32596365", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32596365" } ] }, { "title": "The impact of 2019 novel coronavirus on heart injury: A Systematic review and Meta-analysis.", "journal": "Progress in cardiovascular diseases", "authors": "Li JW, Han TW, Woodward M, Anderson CS, Zhou H, Chen YD, Neal B", "date": "2020-04-20", "evidence": [], "reference": [ { "id": "32305557", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32305557" } ] } ], "biomarker_canonical_id": "AN6400", "score": 2.2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 1 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "f": "frequency", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6402-1", "biomarker_component": [ { "biomarker": "increased CSF1 level", "assessed_biomarker_entity": { "recommended_name": "Macrophage colony-stimulating factor 1", "synonyms": [ { "synonym": "CSF-1" }, { "synonym": "M-CSF" }, { "synonym": "MCSF" }, { "synonym": "Lanimostim" }, { "synonym": "Proteoglycan macrophage colony-stimulating factor" }, { "synonym": "PG-M-CSF" } ] }, "assessed_biomarker_entity_id": "UPKB:P09603", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "23688065", "database": "Pubmed", "url": 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The M-CSF in breast cancer patients were investigated and compared with control groups. The medians of M-CSF, which was 464.28 pg/ml in its levels similarly to the level of the commonly accepted tumor marker, which is CA 15-3 at 25.00 U/ml in the total group of breast cancer patients were significantly higher when compared to the healthy subjects, which is 298.55 pg/ml (p < 0.001). In other words, the median levels of M-CSF in breast cancer total group were statistically higher than in benign breast tumor patients group (p = 0.0004)." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "name": "breast cancer", "description": "A thoracic cancer that originates in the mammary gland.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, "synonyms": [ { "id": "DOID:1612", "name": "malignant tumor of the breast", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "breast tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "mammary cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "primary breast cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "mammary tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "malignant neoplasm of breast", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" } ] }, "evidence_source": [ { "id": "23688065", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/23688065", "evidence_list": [ { "evidence": "Macrophage-colony stimulating factor (M-CSF) regulates growth and differentiation of hematopoietic progenitor cells and functionally activates the maturation of macrophages. The M-CSF in breast cancer patients were investigated and compared with control groups. The medians of M-CSF, which was 464.28 pg/ml in its levels similarly to the level of the commonly accepted tumor marker, which is CA 15-3 at 25.00 U/ml in the total group of breast cancer patients were significantly higher when compared to the healthy subjects, which is 298.55 pg/ml (p < 0.001). In other words, the median levels of M-CSF in breast cancer total group were statistically higher than in benign breast tumor patients group (p = 0.0004)." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "VEGF, M-CSF and CA 15-3 as a new tumor marker panel in breast malignancies: a multivariate analysis with ROC curve.", "journal": "Growth factors (Chur, Switzerland)", "authors": "Ławicki S, Będkowska GE, Szmitkowski M", "date": "2013-05-22", "evidence": [], "reference": [ { "id": "23688065", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/23688065" } ] } ], "biomarker_canonical_id": "AN6402", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "c": "condition", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6403-1", "biomarker_component": [ { "biomarker": "increased KITLG level", "assessed_biomarker_entity": { "recommended_name": "Stem cell factor", "synonyms": [ { "synonym": "Mast cell growth factor" }, { "synonym": "MGF" }, { "synonym": "Stem cell factor" }, { "synonym": "SCF" }, { "synonym": "c-Kit ligand" } ] }, "assessed_biomarker_entity_id": "UPKB:P21583", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "32561706", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32561706", "evidence_list": [ { "evidence": "SCF were significantly higher in fatal than severe and/or mild COVID-19 patients. The temporal changes of the identified CCGFs may serve as biomarkers for prognosis of COVID-19 patients." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32292113", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32292113", "evidence_list": [ { "evidence": "Regulatory DCs (regDCs) play an important role in controlling immune homeostasis and can possess an immunosuppressive ability to induce specific immune tolerance and dampen Th2 type inflammation." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32257537", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32257537", "evidence_list": [ { "evidence": "Therefore, the fact that the transplantation of MSCs improved the outcome of COVID-2019 patients may be due to regulating inflammatory response and promoting tissue repair and regeneration." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:0080600", "recommended_name": { "id": "DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, "synonyms": [ { "id": "DOID:0080600", "name": "SARS-CoV-2 infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan coronavirus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "COVID19", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan seafood market pneumonia virus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019-nCoV infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019 Novel Coronavirus (2019-nCoV)", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" } ] }, "evidence_source": [ { "id": "32561706", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32561706", "evidence_list": [ { "evidence": "SCF were significantly higher in fatal than severe and/or mild COVID-19 patients. The temporal changes of the identified CCGFs may serve as biomarkers for prognosis of COVID-19 patients." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32292113", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32292113", "evidence_list": [ { "evidence": "Regulatory DCs (regDCs) play an important role in controlling immune homeostasis and can possess an immunosuppressive ability to induce specific immune tolerance and dampen Th2 type inflammation." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32257537", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32257537", "evidence_list": [ { "evidence": "Therefore, the fact that the transplantation of MSCs improved the outcome of COVID-2019 patients may be due to regulating inflammatory response and promoting tissue repair and regeneration." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Temporal profiling of plasma cytokines, chemokines and growth factors from mild, severe and fatal COVID-19 patients.", "journal": "Signal transduction and targeted therapy", "authors": "Xu ZS, Shu T, Kang L, Wu D, Zhou X, Liao BW, Sun XL, Zhou X, Wang YY", "date": "2020-06-21", "evidence": [], "reference": [ { "id": "32561706", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32561706" } ] }, { "title": "Stem Cell-Based Therapy for Coronavirus Disease 2019.", "journal": "Stem cells and development", "authors": "Zhao RC", "date": "2020-04-16", "evidence": [], "reference": [ { "id": "32292113", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32292113" } ] }, { "title": "Transplantation of ACE2", "journal": "Aging and disease", "authors": "Leng Z, Zhu R, Hou W, Feng Y, Yang Y, Han Q, Shan G, Meng F, Du D, Wang S, Fan J, Wang W, Deng L, Shi H, Li H, Hu Z, Zhang F, Gao J, Liu H, Li X, Zhao Y, Yin K, He X, Gao Z, Wang Y, Yang B, Jin R, Stambler I, Lim LW, Su H, Moskalev A, Cano A, Chakrabarti S, Min KJ, Ellison-Hughes G, Caruso C, Jin K, Zhao RC", "date": "2020-04-08", "evidence": [], "reference": [ { "id": "32257537", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32257537" } ] } ], "biomarker_canonical_id": "AN6403", "score": 1.4, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 2 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "w": "weight", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6404-1", "biomarker_component": [ { "biomarker": "increase KITLG level", "assessed_biomarker_entity": { "recommended_name": "Stem cell factor", "synonyms": [ { "synonym": "Mast cell growth factor" }, { "synonym": "MGF" }, { "synonym": "Stem cell factor" }, { "synonym": "SCF" }, { "synonym": "c-Kit ligand" } ] }, "assessed_biomarker_entity_id": "UPKB:P21583", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "31254605", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31254605", "evidence_list": [ { "evidence": "Increase in SCF causes a downregulation of certain proteins which induces and activates metastasis in breast cancer patients after surgery. 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SCF triggers the activation of transcription factors involved in cell proliferation, apoptosis and differentiation, which are frequently associated with tumor progression or metastasis." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Adipose derived stem cells promote tumor metastasis in breast Cancer cells by stem cell factor inhibition of miR20b.", "journal": "Cellular signalling", "authors": "Xu H, Li W, Luo S, Yuan J, Hao L", "date": "2019-06-30", "evidence": [], "reference": [ { "id": "31254605", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31254605" } ] } ], "biomarker_canonical_id": "AN6404", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "c": "condition", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6405-1", "biomarker_component": [ { "biomarker": "increased BIL level", "assessed_biomarker_entity": { "recommended_name": "Bilirubin", "synonyms": [ { "synonym": "2,17-diethenyl-1,10,19,22,23,24-hexahydro-3,7,13,18-tetramethyl-1,19-dioxo-21H-biline-8,12-dipropanoic acid" }, { "synonym": "3,18-diethenyl-2,7,13,17-tetramethyl-1,19-dioxo-1,10,19,22,23,24-hexahydro-21H-biline-8,12-dipropanoic acid" }, { "synonym": "bilirubin" }, { "synonym": "8,12-bis(2-carboxyethyl)-2,7,13,17-tetramethyl-3,18-divinylbiladiene-ac-1,19(21H,24H)-dione" }, { "synonym": "Bilirubin" }, { "synonym": "2,7,13,17-tetramethyl-1,19-dioxo-3,18-divinyl-1,10,19,22,23,24-hexahydro-21H-biline-8,12-dipropanoic acid" }, { "synonym": "1,10,19,22,23,24-hexahydro-2,7,13,17-tetramethyl-1,19-dioxo-3,18-divinylbiline-8,12-dipropionic acid" }, { "synonym": "bilirubin(Z,Z)" }, { "synonym": "bilirubin-IXalpha" } ] }, "assessed_biomarker_entity_id": "CHEBI:16990", "assessed_entity_type": "metabolite", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "33898-8" } ], "evidence_source": [ { "id": "32509218", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32509218", "evidence_list": [ { "evidence": "This study found that the increased level of serum bilirubin correlates with better prognosis in patients with EOC. 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"resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019-nCoV infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019 Novel Coronavirus (2019-nCoV)", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" } ] }, "evidence_source": [ { "id": "32492406", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32492406", "evidence_list": [ { "evidence": "In a proteomic investigation of sera in SARS patients, decreasing PF4 was found to be associated with poor prognosis which is in consistent with our findings in COVID-19." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Proteomic and Metabolomic Characterization of COVID-19 Patient Sera.", "journal": "Cell", "authors": "Shen B, Yi X, Sun Y, Bi X, Du J, Zhang C, Quan S, Zhang F, Sun R, Qian L, Ge W, Liu W, Liang S, Chen H, Zhang Y, Li J, Xu J, He Z, Chen B, Wang J, Yan H, Zheng Y, Wang D, Zhu J, Kong Z, Kang Z, Liang X, Ding X, Ruan G, Xiang N, Cai X, Gao H, Li L, Li S, Xiao Q, Lu T, Zhu Y, Liu H, Chen H, Guo T", "date": "2020-06-04", "evidence": [], "reference": [ { "id": "32492406", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32492406" } ] } ], "biomarker_canonical_id": "AN6406", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "f": "frequency", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6407-1", "biomarker_component": [ { "biomarker": "presence of rs12674822 in ANGP2", "assessed_biomarker_entity": { "recommended_name": "Angiopoietin-2 gene", 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Our data demonstrate that levels of serum HE4, CYFRA21-1, CEA, CA125, CA153, SCC, and NSE are positively associated with CRP, a crucial factor in correlation with the severity of the disease. We concluded that elevations of serum cancer biomarkers positively correlated with the pathological progressions of COVID-19, demonstrating diffuse and acute pathophysiological injuries in COVID-19." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32504736", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32504736", "evidence_list": [ { "evidence": "Tumor biomarkers, such as carcinoembryonic antigen (CEA), cytokeratin 19 fragment (CYFRA21-1), neuron-specific enolase (NSE), squamous cell carcinoma antigen (SCCA) and Pro-Gastrin Releasing Peptide (ProGRP), were elevated." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32504736", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32504736", "evidence_list": [ { "evidence": "In short, we concluded that the concentrations of tumor biomarkers of CEA, CYFRA21-1, NSE, SCCA, ProGRP were elevated in COVID-19 patients, and that CEA, CYFRA21-1, SCCA could predicte the clinical outcome of COVID-19 patients." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32347972", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32347972", "evidence_list": [ { "evidence": "Presence of elevated NSE levels shown as predictor of COVID-19 severity." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "16033098", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/16033098", "evidence_list": [ { "evidence": "Tumor marker serum levels were related to histological type and tumor extension, with ProGRP being the most sensitive marker in SCLC, CEA in adenocarcinomas and CYFRA 21-1 in squamous tumors. The most sensitive combinations of tumor markers were ProGRP and NSE in SCLC (88%), and CEA plus CYFRA in NSCLC (82%). In summary, ProGRP is the tumor marker of choice in SCLC and NSE is a complementary tumor marker in this histological type." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "16062024", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/16062024", "evidence_list": [ { "evidence": "Alteration of serum tumor markers cytokeratin 19 fragment, carcinoembryonic antigen and neuron-specific enolase is associated with particular tumor histology, smoking habit, more advanced disease and poor prognosis. The number of patients with elevated levels of cytokeratin 19 fragment and neuron-specific enolase was higher in more advanced disease than in early lung cancer (p=0.036 and p=0.036, respectively). Preoperative levels of cytokeratin 19 fragment (p=0.017 and p=0.016, respectively) and neuron-specific enolase (p=0.03 and p=0.006, respectively) were significantly associated with more advanced disease and tumor size, as well as tumor histology in non-small cell lung cancer (p=0.03 and p=0.016, respectively)." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "30994045", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30994045", "evidence_list": [ { "evidence": "Our results confirm that patients with lung cancer have increased serum levels of CEA, CYFRA 21-1, ProGRP, and NSE compared to patients with benign disease. Moreover, we found a strong association among the SCLC patients and high levels of ProGRP and NSE." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "name": "COVID-19", "description": "A respiratory system cancer that is located_in the lung.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1324" }, "synonyms": [] }, "evidence_source": [ { "id": "32504736", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32504736", "evidence_list": [ { "evidence": "In short, we concluded that the concentrations of tumor biomarkers of CEA, CYFRA21-1, NSE, SCCA, ProGRP were elevated in COVID-19 patients, and that CEA, CYFRA21-1, SCCA could predicte the clinical outcome of COVID-19 patients." }, { "evidence": "Tumor biomarkers, such as carcinoembryonic antigen (CEA), cytokeratin 19 fragment (CYFRA21-1), neuron-specific enolase (NSE), squamous cell carcinoma antigen (SCCA) and Pro-Gastrin Releasing Peptide (ProGRP), were elevated." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32347972", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32347972", "evidence_list": [ { "evidence": "This is the first report with such a substantial evaluation of cancer biomarkers on a large patient population of COVID-19. Our data demonstrate that levels of serum HE4, CYFRA21-1, CEA, CA125, CA153, SCC, and NSE are positively associated with CRP, a crucial factor in correlation with the severity of the disease. We concluded that elevations of serum cancer biomarkers positively correlated with the pathological progressions of COVID-19, demonstrating diffuse and acute pathophysiological injuries in COVID-19." }, { "evidence": "Presence of elevated NSE levels shown as predictor of COVID-19 severity." } ], "tags": [ { "tag": "condition" }, { "tag": "best_biomarker_role" } ] }, { "id": "16033098", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/16033098", "evidence_list": [ { "evidence": "Tumor marker serum levels were related to histological type and tumor extension, with ProGRP being the most sensitive marker in SCLC, CEA in adenocarcinomas and CYFRA 21-1 in squamous tumors. The most sensitive combinations of tumor markers were ProGRP and NSE in SCLC (88%), and CEA plus CYFRA in NSCLC (82%). In summary, ProGRP is the tumor marker of choice in SCLC and NSE is a complementary tumor marker in this histological type." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "16062024", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/16062024", "evidence_list": [ { "evidence": "Alteration of serum tumor markers cytokeratin 19 fragment, carcinoembryonic antigen and neuron-specific enolase is associated with particular tumor histology, smoking habit, more advanced disease and poor prognosis. The number of patients with elevated levels of cytokeratin 19 fragment and neuron-specific enolase was higher in more advanced disease than in early lung cancer (p=0.036 and p=0.036, respectively). Preoperative levels of cytokeratin 19 fragment (p=0.017 and p=0.016, respectively) and neuron-specific enolase (p=0.03 and p=0.006, respectively) were significantly associated with more advanced disease and tumor size, as well as tumor histology in non-small cell lung cancer (p=0.03 and p=0.016, respectively)." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "30994045", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30994045", "evidence_list": [ { "evidence": "Our results confirm that patients with lung cancer have increased serum levels of CEA, CYFRA 21-1, ProGRP, and NSE compared to patients with benign disease. Moreover, we found a strong association among the SCLC patients and high levels of ProGRP and NSE." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Elevations of serum cancer biomarkers correlate with severity of COVID-19.", "journal": "Journal of medical virology", "authors": "Wei X, Su J, Yang K, Wei J, Wan H, Cao X, Tan W, Wang H", "date": "2020-04-30", "evidence": [], "reference": [ { "id": "32347972", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32347972" } ] }, { "title": "Tumor biomarkers predict clinical outcome of COVID-19 patients.", "journal": "The Journal of infection", "authors": "He B, Zhong A, Wu Q, Liu X, Lin J, Chen C, He Y, Guo Y, Zhang M, Zhu P, Wu J, Wang C, Wang S, Xia X", "date": "2020-06-07", "evidence": [], "reference": [ { "id": "32504736", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32504736" } ] }, { "title": "Pro-gastrin-releasing peptide (proGRP) in patients with benign and malignant diseases: comparison with CEA, SCC, CYFRA 21-1 and NSE in patients with lung cancer.", "journal": "Anticancer research", "authors": "Molina R, Auge JM, Filella X, Viñolas N, Alicarte J, Domingo JM, Ballesta AM", "date": "2005-07-22", "evidence": [], "reference": [ { "id": "16033098", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/16033098" } ] }, { "title": "[Clinical and prognostic significance of tumor markers cytokeratin 19 fragment, carcinoembryonic antigen, and neuron-specific enolase in lung cancer].", "journal": "Medicina (Kaunas, Lithuania)", "authors": "Zemaitis M, Sakalauskas R, Malakauskas K, Muley T, Fischer JR, Lahm H", "date": "2005-08-03", "evidence": [], "reference": [ { "id": "16062024", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/16062024" } ] }, { "title": "New and old biomarkers in the differential diagnosis of lung cancer: Pro-gastrin-releasing peptide in comparison with neuron-specific enolase, carcinoembryonic antigen, and CYFRA 21-1.", "journal": "The International journal of biological markers", "authors": "Mauro C, Passerini R, Spaggiari L, Galetta D, Radice D, Lentati P, Sandri MT", "date": "2019-04-18", "evidence": [], "reference": [ { "id": "30994045", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30994045" } ] } ], "biomarker_canonical_id": "AN6408", "score": 2.8, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 4 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "c": "condition", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6756-1", "biomarker_component": [ { "biomarker": "Elevated CEA levels", "assessed_biomarker_entity": { "recommended_name": "Carcinoembryonic antigen", "synonyms": [ { "synonym": "Carcinoembryonic antigen" }, { "synonym": "CEA" }, { "synonym": "Meconium antigen 100" } ] }, "assessed_biomarker_entity_id": "UPKB:P06731", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "19193-2" } ], "evidence_source": [ { "id": "16062024", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/16062024", "evidence_list": [ { "evidence": "Cytokeratin 19 fragment, carcinoembryonic antigen, and neuron-specific enolase were elevated in 19.6%, 43.5%, and 63% of patients, respectively." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] }, { "biomarker": "increased CEA level", "assessed_biomarker_entity": { "recommended_name": "Carcinoembryonic antigen", "synonyms": [ { "synonym": "Carcinoembryonic antigen" }, { "synonym": "CEA" }, { "synonym": "Meconium antigen 100" } ] }, "assessed_biomarker_entity_id": "UPKB: P06731", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "19193-2" } ], "evidence_source": [ { "id": "30994045", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30994045", "evidence_list": [ { "evidence": "Our results confirm that patients with lung cancer have increased serum levels of CEA, CYFRA 21-1, ProGRP, and NSE compared to patients with benign disease. Moreover, we found a strong association among the SCLC patients and high levels of ProGRP and NSE." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1324" }, "synonyms": [] }, "evidence_source": [ { "id": "16062024", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/16062024", "evidence_list": [ { "evidence": "Cytokeratin 19 fragment, carcinoembryonic antigen, and neuron-specific enolase were elevated in 19.6%, 43.5%, and 63% of patients, respectively." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "30994045", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30994045", "evidence_list": [ { "evidence": "Our results confirm that patients with lung cancer have increased serum levels of CEA, CYFRA 21-1, ProGRP, and NSE compared to patients with benign disease. Moreover, we found a strong association among the SCLC patients and high levels of ProGRP and NSE." } ], "tags": [ { "tag": "condition" }, { "tag": "best_biomarker_role" } ] } ], "citation": [ { "title": "[Clinical and prognostic significance of tumor markers cytokeratin 19 fragment, carcinoembryonic antigen, and neuron-specific enolase in lung cancer].", "journal": "Medicina (Kaunas, Lithuania)", "authors": "Zemaitis M, Sakalauskas R, Malakauskas K, Muley T, Fischer JR, Lahm H", "date": "2005-08-03", "evidence": [], "reference": [ { "id": "16062024", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/16062024" } ] }, { "title": "New and old biomarkers in the differential diagnosis of lung cancer: Pro-gastrin-releasing peptide in comparison with neuron-specific enolase, carcinoembryonic antigen, and CYFRA 21-1.", "journal": "The International journal of biological markers", "authors": "Mauro C, Passerini R, Spaggiari L, Galetta D, Radice D, Lentati P, Sandri MT", "date": "2019-04-18", "evidence": [], "reference": [ { "id": "30994045", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30994045" } ] } ], "biomarker_canonical_id": "AN6756", "score": 2.2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 1 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6411-1", "biomarker_component": [ { "biomarker": "increased PROGRP level", "assessed_biomarker_entity": { "recommended_name": "Progastrin releasing peptide", "synonyms": [] }, "assessed_biomarker_entity_id": "PRO:PR_000050383", "assessed_entity_type": "peptide", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": 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patients.", "journal": "The Journal of infection", "authors": "He B, Zhong A, Wu Q, Liu X, Lin J, Chen C, He Y, Guo Y, Zhang M, Zhu P, Wu J, Wang C, Wang S, Xia X", "date": "2020-06-07", "evidence": [], "reference": [ { "id": "32504736", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32504736" } ] } ], "biomarker_canonical_id": "AN6411", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6412-1", "biomarker_component": [ { "biomarker": "decreased SaO2 level", "assessed_biomarker_entity": { "recommended_name": "Oxygen saturation", "synonyms": [] }, "assessed_biomarker_entity_id": "NCIt:C60832", 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Multivariable analysis showed that only VWF: Ag was a predictive biomarker for HCC development." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "von Willebrand factor is a useful biomarker for liver fibrosis and prediction of hepatocellular carcinoma development in patients with hepatitis B and C.", "journal": "United European gastroenterology journal", "authors": "Takaya H, Kawaratani H, Tsuji Y, Nakanishi K, Saikawa S, Sato S, Sawada Y, Kaji K, Okura Y, Shimozato N, Kitade M, Akahane T, Moriya K, Namisaki T, Mitoro A, Matsumoto M, Fukui H, Yoshiji H", "date": "2018-11-06", "evidence": [], "reference": [ { "id": "30386613", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30386613" } ] } ], "biomarker_canonical_id": "AN6429", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6430-1", "biomarker_component": [ { "biomarker": "increased SELP level", "assessed_biomarker_entity": { "recommended_name": "P-selectin", "synonyms": [ { "synonym": "CD62 antigen-like family member P" }, { "synonym": "Granule membrane protein 140" }, { "synonym": "GMP-140" }, { "synonym": "Leukocyte-endothelial cell adhesion molecule 3" }, { "synonym": "LECAM3" }, { "synonym": "Platelet activation dependent granule-external membrane protein" }, { "synonym": "PADGEM" } ] }, "assessed_biomarker_entity_id": "UPKB:P16109", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "17181-9" } ], "evidence_source": [ { "id": "32757722", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32757722", "evidence_list": [ { "evidence": "Biomarkers of platelet activity and vascular health are significantly associated with the composite outcome of thrombosis or death in hospitalized patients with COVID-19. 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Together, these results provide biochemical evidence that endotheliopathy and platelet activation are ubiquitous in COVID-19-associated coagulopathy and might play key roles in the progression of disease." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:0080600", "recommended_name": { "id": "DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, "synonyms": [ { "id": "DOID:0080600", "name": "SARS-CoV-2 infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan coronavirus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "COVID19", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan seafood market pneumonia virus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019-nCoV infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019 Novel Coronavirus (2019-nCoV)", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" } ] }, "evidence_source": [ { "id": "32757722", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32757722", "evidence_list": [ { "evidence": "Biomarkers of platelet activity and vascular health are significantly associated with the composite outcome of thrombosis or death in hospitalized patients with COVID-19. P-selectin and sCD40L contribute to thrombosis by supporting platelet-myeloid heteroaggregate formation and thrombi stability by interaction with PSGL-1 and alpha IIb beta3, respectively." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32619411", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32619411", "evidence_list": [ { "evidence": "We also show that critical illness is associated with further elevations in VWF, as well as increases in soluble P-selectin and sCD40L when compared with controls. Together, these results provide biochemical evidence that endotheliopathy and platelet activation are ubiquitous in COVID-19-associated coagulopathy and might play key roles in the progression of disease." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Platelet and Vascular Biomarkers Associate With Thrombosis and Death in Coronavirus Disease.", "journal": "Circulation research", "authors": "Barrett TJ, Lee AH, Xia Y, Lin LH, Black M, Cotzia P, Hochman J, Berger JS", "date": "2020-08-08", "evidence": [], "reference": [ { "id": "32757722", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32757722" } ] }, { "title": "Endotheliopathy in COVID-19-associated coagulopathy: evidence from a single-centre, cross-sectional study.", "journal": "The Lancet. Haematology", "authors": "Goshua G, Pine AB, Meizlish ML, Chang CH, Zhang H, Bahel P, Baluha A, Bar N, Bona RD, Burns AJ, Dela Cruz CS, Dumont A, Halene S, Hwa J, Koff J, Menninger H, Neparidze N, Price C, Siner JM, Tormey C, Rinder HM, Chun HJ, Lee AI", "date": "2020-07-04", "evidence": [], "reference": [ { "id": "32619411", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32619411" } ] } ], "biomarker_canonical_id": "AN6430", "score": 2.2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 1 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "f": "frequency", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6431-1", "biomarker_component": [ { "biomarker": "increased CD40LG level", "assessed_biomarker_entity": { "recommended_name": "CD40 ligand", "synonyms": [ { "synonym": "CD40-L" }, { "synonym": "T-cell antigen Gp39" }, { "synonym": "TNF-related activation protein" }, { "synonym": "TRAP" }, { "synonym": "Tumor necrosis factor ligand superfamily member 5" } ] }, "assessed_biomarker_entity_id": "UPKB:P29965", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "14760083", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/14760083", "evidence_list": [ { "evidence": "Patients with lung cancer had median sCD40L levels higher than in control subjects (0.46 versus 0.13 ng/ml; P < 0.0001), although correlation with the stage of disease was not evident. Nonetheless, sCD40L levels were significantly higher in squamous cancer compared with adenocarcinoma (0.75 versus 0.27 ng/ml; P < 0.05). Moreover, median sCD40L levels were higher in stage IV compared with nonmetastatic squamous lung cancer (1.02 versus 0.61 ng/ml; P < 0.05). sCD40L levels significantly correlated with sP-selectin (P < 0.001), prothrombin fragment 1 + 2 (P < 0.001), or thrombin-antithrombin III complex (P < 0.05) in squamous lung cancer, but only sP-selectin (P = 0.011) was independently related to sCD40L." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1324" }, "synonyms": [] }, "evidence_source": [ { "id": "14760083", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/14760083", "evidence_list": [ { "evidence": "Patients with lung cancer had median sCD40L levels higher than in control subjects (0.46 versus 0.13 ng/ml; P < 0.0001), although correlation with the stage of disease was not evident. Nonetheless, sCD40L levels were significantly higher in squamous cancer compared with adenocarcinoma (0.75 versus 0.27 ng/ml; P < 0.05). Moreover, median sCD40L levels were higher in stage IV compared with nonmetastatic squamous lung cancer (1.02 versus 0.61 ng/ml; P < 0.05). sCD40L levels significantly correlated with sP-selectin (P < 0.001), prothrombin fragment 1 + 2 (P < 0.001), or thrombin-antithrombin III complex (P < 0.05) in squamous lung cancer, but only sP-selectin (P = 0.011) was independently related to sCD40L." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Soluble CD40 ligand plasma levels in lung cancer.", "journal": "Clinical cancer research : an official journal of the American Association for Cancer Research", "authors": "Roselli M, Mineo TC, Basili S, Martini F, Mariotti S, Aloe S, Del Monte G, Ambrogi V, Spila A, Palmirotta R, D'Alessandro R, Davì G, Guadagni F, Ferroni P", "date": "2004-02-05", "evidence": [], "reference": [ { "id": "14760083", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/14760083" } ] } ], "biomarker_canonical_id": "AN6431", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "c": "condition", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6431-2", "biomarker_component": [ { "biomarker": "increased CD40LG level", "assessed_biomarker_entity": { "recommended_name": "CD40 ligand", "synonyms": [ { "synonym": "CD40-L" }, { "synonym": "T-cell antigen Gp39" }, { "synonym": "TNF-related activation protein" }, { "synonym": "TRAP" }, { "synonym": "Tumor necrosis factor ligand superfamily member 5" } ] }, "assessed_biomarker_entity_id": "UPKB:P29965", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "24745825", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/24745825", "evidence_list": [ { "evidence": "Serum sCD40L levels were significantly higher in PDAC group compared with non-cancer groups in both training (p < 0.05) and validation (p < 0.05 datasets. Kaplan-Meier survival analysis demonstrated patients with high-serum sCD40L (> 35,000 ng/ml) had a poorer prognosis than those with low serum sCD40L (log-rank, p = 0.015). Serum sCD40L is correlated with immunosuppression and angiogenesis in PDAC carcinogenesis/progression, and is a promising diagnostic and prognostic biomarker for PDAC superior to CA19-9 and CEA." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:1793", "recommended_name": { "id": "DOID:1793", "name": "pancreatic cancer", "description": "An endocrine gland cancer located_in the pancreas.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, "synonyms": [ { "id": "DOID:1793", "name": "Ca head of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "Ca body of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "pancreatic tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "malignant neoplasm of tail of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "malignant neoplasm of head of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "pancreatic neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "Ca tail of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "pancreas neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "malignant neoplasm of body of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" } ] }, "evidence_source": [ { "id": "24745825", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/24745825", "evidence_list": [ { "evidence": "Serum sCD40L levels were significantly higher in PDAC group compared with non-cancer groups in both training (p < 0.05) and validation (p < 0.05 datasets. Kaplan-Meier survival analysis demonstrated patients with high-serum sCD40L (> 35,000 ng/ml) had a poorer prognosis than those with low serum sCD40L (log-rank, p = 0.015). Serum sCD40L is correlated with immunosuppression and angiogenesis in PDAC carcinogenesis/progression, and is a promising diagnostic and prognostic biomarker for PDAC superior to CA19-9 and CEA." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Clinical significance of elevated serum soluble CD40 ligand levels as a diagnostic and prognostic tumor marker for pancreatic ductal adenocarcinoma.", "journal": "Journal of translational medicine", "authors": "Chung HW, Lim JB", "date": "2014-04-22", "evidence": [], "reference": [ { "id": "24745825", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/24745825" } ] } ], "biomarker_canonical_id": "AN6431", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "c": "condition", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6431-3", "biomarker_component": [ { "biomarker": "increased CD40LG level", "assessed_biomarker_entity": { "recommended_name": "CD40 ligand", "synonyms": [ { "synonym": "CD40-L" }, { "synonym": "T-cell antigen Gp39" }, { "synonym": "TNF-related activation protein" }, { "synonym": "TRAP" }, { "synonym": "Tumor necrosis factor ligand superfamily member 5" } ] }, "assessed_biomarker_entity_id": "UPKB:P29965", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "32619411", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32619411", "evidence_list": [ { "evidence": "We also show that critical illness is associated with further elevations in VWF, as well as increases in soluble P-selectin and sCD40L when compared with controls. Together, these results provide biochemical evidence that endotheliopathy and platelet activation are ubiquitous in COVID-19-associated coagulopathy and might play key roles in the progression of disease." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "32757722", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32757722", "evidence_list": [ { "evidence": "Biomarkers of platelet activity and vascular health are significantly associated with the composite outcome of thrombosis or death in hospitalized patients with COVID-19. P-selectin and sCD40L contribute to thrombosis by supporting platelet-myeloid heteroaggregate formation and thrombi stability by interaction with PSGL-1 and alpha IIb beta3, respectively." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "monitoring" } ], "condition": { "id": "DOID:0080600", "recommended_name": { "id": "DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, "synonyms": [ { "id": "DOID:0080600", "name": "SARS-CoV-2 infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan coronavirus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "COVID19", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan seafood market pneumonia virus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019-nCoV infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019 Novel Coronavirus (2019-nCoV)", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" } ] }, "evidence_source": [ { "id": "32619411", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32619411", "evidence_list": [ { "evidence": "We also show that critical illness is associated with further elevations in VWF, as well as increases in soluble P-selectin and sCD40L when compared with controls. Together, these results provide biochemical evidence that endotheliopathy and platelet activation are ubiquitous in COVID-19-associated coagulopathy and might play key roles in the progression of disease." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32757722", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32757722", "evidence_list": [ { "evidence": "Biomarkers of platelet activity and vascular health are significantly associated with the composite outcome of thrombosis or death in hospitalized patients with COVID-19. P-selectin and sCD40L contribute to thrombosis by supporting platelet-myeloid heteroaggregate formation and thrombi stability by interaction with PSGL-1 and alpha IIb beta3, respectively." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Endotheliopathy in COVID-19-associated coagulopathy: evidence from a single-centre, cross-sectional study.", "journal": "The Lancet. Haematology", "authors": "Goshua G, Pine AB, Meizlish ML, Chang CH, Zhang H, Bahel P, Baluha A, Bar N, Bona RD, Burns AJ, Dela Cruz CS, Dumont A, Halene S, Hwa J, Koff J, Menninger H, Neparidze N, Price C, Siner JM, Tormey C, Rinder HM, Chun HJ, Lee AI", "date": "2020-07-04", "evidence": [], "reference": [ { "id": "32619411", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32619411" } ] }, { "title": "Platelet and Vascular Biomarkers Associate With Thrombosis and Death in Coronavirus Disease.", "journal": "Circulation research", "authors": "Barrett TJ, Lee AH, Xia Y, Lin LH, Black M, Cotzia P, Hochman J, Berger JS", "date": "2020-08-08", "evidence": [], "reference": [ { "id": "32757722", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32757722" } ] } ], "biomarker_canonical_id": "AN6431", "score": 1.2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 1 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "f": "frequency", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6432-1", "biomarker_component": [ { "biomarker": "increased THBD level", "assessed_biomarker_entity": { "recommended_name": "Thrombomodulin", "synonyms": [ { "synonym": "TM" }, { "synonym": "Fetomodulin" } ] }, "assessed_biomarker_entity_id": "UPKB:P07204", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "11570577", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/11570577", "evidence_list": [ { "evidence": "The preoperative plasma TM level of patients with HCC (10.2+/-5.7 ng/ml) was significantly higher than that of those patients with benign liver-occupying lesion (6.1+/-2.2 ng/ml) and that of normal controls (5.7+/-1.0 ng/ml), respectively (P<0.05). Plasma TM increases in patients with HCC and can be a biomarker of the formation of PVTT." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:3571", "recommended_name": { "id": "DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, "synonyms": [ { "id": "DOID:3571", "name": "resectable malignant neoplasm of the liver", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "primary liver cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "Resectable malignant neoplasm of Liver", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "neoplasm of liver", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "malignant tumor of liver", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "malignant neoplasm of liver, primary", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "Ca liver - primary", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "primary malignant neoplasm of liver", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "hepatic neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "hepatic cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "malignant hepato-biliary neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "malignant neoplasm of liver", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" } ] }, "evidence_source": [ { "id": "11570577", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/11570577", "evidence_list": [ { "evidence": "The preoperative plasma TM level of patients with HCC (10.2+/-5.7 ng/ml) was significantly higher than that of those patients with benign liver-occupying lesion (6.1+/-2.2 ng/ml) and that of normal controls (5.7+/-1.0 ng/ml), respectively (P<0.05). Plasma TM increases in patients with HCC and can be a biomarker of the formation of PVTT." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "The potential of plasma thrombomodulin as a biomarker of portal vein tumor thrombus in hepatocellular carcinoma.", "journal": "Journal of cancer research and clinical oncology", "authors": "Zhou J, Tang ZY, Fan J, Wu ZQ, Ji Y, Ye SL", "date": "2001-09-26", "evidence": [], "reference": [ { "id": "11570577", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/11570577" } ] } ], "biomarker_canonical_id": "AN6432", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "f": "frequency", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6433-1", "biomarker_component": [ { "biomarker": "decreased THBD level", "assessed_biomarker_entity": { "recommended_name": "Thrombomodulin", "synonyms": [ { "synonym": "AHUS6" }, { "synonym": "BDCA-3" }, { "synonym": "BDCA3" }, { "synonym": "CD141" }, { "synonym": "THPH12" }, { "synonym": "THRM" }, { "synonym": "TM" } ] }, "assessed_biomarker_entity_id": "NCBI: 7056", "assessed_entity_type": "gene", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "23918310", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/23918310", "evidence_list": [ { "evidence": "The migratory ability of ovarian cancer cells was enhanced dramatically after TM silencing. TM overexpression in ovarian cells suppressed the proliferation and migration capability. Furthermore, we found that skov-3 cells treated with TM shRNA expressed high levels of fibronectin and vimentin and that the expression of these markers correlated positively with their migratory ability. Our results demonstrate that TM expression may regulate cell growth and migration in ovarian cancer cells. This finding suggests that TM may be a novel prognostic and therapeutic target for ovarian cancer." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:2394", "recommended_name": { "id": "DOID:2394", "name": "ovarian cancer", "description": "A female reproductive organ cancer that is located_in the ovary.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, "synonyms": [ { "id": "DOID:2394", "name": "primary ovarian cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "tumor of the Ovary", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "ovary neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "malignant tumour of ovary", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "malignant Ovarian tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "ovarian neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" } ] }, "evidence_source": [ { "id": "23918310", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/23918310", "evidence_list": [ { "evidence": "The migratory ability of ovarian cancer cells was enhanced dramatically after TM silencing. TM overexpression in ovarian cells suppressed the proliferation and migration capability. Furthermore, we found that skov-3 cells treated with TM shRNA expressed high levels of fibronectin and vimentin and that the expression of these markers correlated positively with their migratory ability. Our results demonstrate that TM expression may regulate cell growth and migration in ovarian cancer cells. This finding suggests that TM may be a novel prognostic and therapeutic target for ovarian cancer." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Thrombomodulin mediates the progression of epithelial ovarian cancer cells.", "journal": "Tumour biology : the journal of the International Society for Oncodevelopmental Biology and Medicine", "authors": "Chen LM, Wang W, Lee JC, Chiu FH, Wu CT, Tai CJ, Wang CK, Tai CJ, Huang MT, Chang YJ", "date": "2013-08-07", "evidence": [], "reference": [ { "id": "23918310", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/23918310" } ] } ], "biomarker_canonical_id": "AN6433", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6432-2", "biomarker_component": [ { "biomarker": "increased THBD level", "assessed_biomarker_entity": { "recommended_name": "Thrombomodulin", "synonyms": [ { "synonym": "TM" }, { "synonym": "Fetomodulin" } ] }, "assessed_biomarker_entity_id": "UPKB:P07204", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "32619411", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32619411", "evidence_list": [ { "evidence": "In all patients, soluble thrombomodulin concentrations greater than 3.26 ng/mL were associated with lower rates of hospital discharge (22 [88%] of 25 patients with low concentrations vs 13 [52%] of 25 patients with high concentrations; p=0.0050) and lower likelihood of survival on Kaplan-Meier analysis (hazard ratio 5.9, 95% CI 1.9-18.4; p=0.0087)." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:0080600", "recommended_name": { "id": "DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, "synonyms": [ { "id": "DOID:0080600", "name": "SARS-CoV-2 infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan coronavirus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "COVID19", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan seafood market pneumonia virus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019-nCoV infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019 Novel Coronavirus (2019-nCoV)", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" } ] }, "evidence_source": [ { "id": "32619411", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32619411", "evidence_list": [ { "evidence": "In all patients, soluble thrombomodulin concentrations greater than 3.26 ng/mL were associated with lower rates of hospital discharge (22 [88%] of 25 patients with low concentrations vs 13 [52%] of 25 patients with high concentrations; p=0.0050) and lower likelihood of survival on Kaplan-Meier analysis (hazard ratio 5.9, 95% CI 1.9-18.4; p=0.0087)." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Endotheliopathy in COVID-19-associated coagulopathy: evidence from a single-centre, cross-sectional study.", "journal": "The Lancet. Haematology", "authors": "Goshua G, Pine AB, Meizlish ML, Chang CH, Zhang H, Bahel P, Baluha A, Bar N, Bona RD, Burns AJ, Dela Cruz CS, Dumont A, Halene S, Hwa J, Koff J, Menninger H, Neparidze N, Price C, Siner JM, Tormey C, Rinder HM, Chun HJ, Lee AI", "date": "2020-07-04", "evidence": [], "reference": [ { "id": "32619411", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32619411" } ] } ], "biomarker_canonical_id": "AN6432", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "c": "condition", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6434-1", "biomarker_component": [ { "biomarker": "increased EDN1 level", "assessed_biomarker_entity": { "recommended_name": "Endothelin-1", "synonyms": [ { "synonym": "Preproendothelin-1" }, { "synonym": "PPET1" } ] }, "assessed_biomarker_entity_id": "UPKB:P05305", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "26537720", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/26537720", "evidence_list": [ { "evidence": "Serum big ET-1 levels may be useful as a diagnostic tool in OSCC and as an adjunct to OSCC staging. By comparing the mean of the big ET-1 concentrations of cases and controls, the independent t-test revealed significant higher big ET-1 concentration of OSCC cases when compared to controls (p<0.0001)." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:11934", "recommended_name": { "id": "DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11934" }, "synonyms": [ { "id": "DOID:11934", "name": "head and neck neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11934" }, { "id": "DOID:11934", "name": "head/neck neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11934" }, { "id": "DOID:11934", "name": "head and neck tumours", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11934" }, { "id": "DOID:11934", "name": "tumor of head and neck", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11934" } ] }, "evidence_source": [ { "id": "26537720", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/26537720", "evidence_list": [ { "evidence": "Serum big ET-1 levels may be useful as a diagnostic tool in OSCC and as an adjunct to OSCC staging. By comparing the mean of the big ET-1 concentrations of cases and controls, the independent t-test revealed significant higher big ET-1 concentration of OSCC cases when compared to controls (p<0.0001)." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Serum big endothelin-1 as a biomarker in oral squamous cell carcinoma patients: an analytical study.", "journal": "Journal of applied oral science : revista FOB", "authors": "Mankapure PK, Barpande SR, Bhavthankar JD, Mandale M", "date": "2015-11-06", "evidence": [], "reference": [ { "id": "26537720", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/26537720" } ] } ], "biomarker_canonical_id": "AN6434", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6380-2", "biomarker_component": [ { "biomarker": "increased CFDNA level", "assessed_biomarker_entity": { "recommended_name": "Cell-free DNA", "synonyms": [] }, "assessed_biomarker_entity_id": "NCIt:C128274", "assessed_entity_type": "DNA", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "75605-6" } ], "evidence_source": [ { "id": "29175734", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/29175734", "evidence_list": [ { "evidence": "Baseline cfDNA concentration correlated with pre-treatment tumour burden (p = 0.52, P < 0.001). Baseline cfDNA levels correlated significantly with hazard of death and overall survival, and a cut off value of 89 pg/ul identified two distinct prognostic groups (HR = 2.22 for high cfDNA, P = 0.004). Patients with cfDNA 89 pg/ul had shorter OS (10.0 versus 22.7 months, P = 0.009; HR = 2.22 for high cfDNA, P = 0.004) In addition, the ratio between baseline cfDNA and tumour burden was prognostic (HR = 2.7 for cfDNA/tumour volume 8 pg/(l*cm3), P = 0.024). Plasma cfDNA level correlates to tumour volume and is a surrogate biomarker for tumour burden and a prognostic marker for survival in metastatic melanoma patients." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_4159" }, "synonyms": [ { "id": "DOID:4159", "name": "CA - skin cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_4159" }, { "id": "DOID:4159", "name": "malignant neoplasm of skin", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_4159" }, { "id": "DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_4159" } ] }, "evidence_source": [ { "id": "29175734", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/29175734", "evidence_list": [ { "evidence": "Baseline cfDNA concentration correlated with pre-treatment tumour burden (p = 0.52, P < 0.001). Baseline cfDNA levels correlated significantly with hazard of death and overall survival, and a cut off value of 89 pg/ul identified two distinct prognostic groups (HR = 2.22 for high cfDNA, P = 0.004). Patients with cfDNA 89 pg/ul had shorter OS (10.0 versus 22.7 months, P = 0.009; HR = 2.22 for high cfDNA, P = 0.004) In addition, the ratio between baseline cfDNA and tumour burden was prognostic (HR = 2.7 for cfDNA/tumour volume 8 pg/(l*cm3), P = 0.024). Plasma cfDNA level correlates to tumour volume and is a surrogate biomarker for tumour burden and a prognostic marker for survival in metastatic melanoma patients." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Plasma total cell-free DNA (cfDNA) is a surrogate biomarker for tumour burden and a prognostic biomarker for survival in metastatic melanoma patients.", "journal": "European journal of cancer (Oxford, England : 1990)", "authors": "Valpione S, Gremel G, Mundra P, Middlehurst P, Galvani E, Girotti MR, Lee RJ, Garner G, Dhomen N, Lorigan PC, Marais R", "date": "2017-11-28", "evidence": [], "reference": [ { "id": "29175734", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/29175734" } ] } ], "biomarker_canonical_id": "AN6380", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "c": "condition", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6380-3", "biomarker_component": [ { "biomarker": "increased CFDNA level", "assessed_biomarker_entity": { "recommended_name": "Cell-free DNA", "synonyms": [] }, "assessed_biomarker_entity_id": "NCIt:C128274", "assessed_entity_type": "DNA", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "32329756", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32329756", "evidence_list": [ { "evidence": "Cell-free DNA strongly correlated with absolute neutrophil count. In summary, these data reveal high levels of NETs in many patients with COVID-19, where they may contribute to cytokine release and respiratory failure." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:0080600", "recommended_name": { "id": "DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, "synonyms": [ { "id": "DOID:0080600", "name": "SARS-CoV-2 infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan coronavirus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "COVID19", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan seafood market pneumonia virus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019-nCoV infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019 Novel Coronavirus (2019-nCoV)", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" } ] }, "evidence_source": [ { "id": "32329756", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32329756", "evidence_list": [ { "evidence": "Cell-free DNA strongly correlated with absolute neutrophil count. In summary, these data reveal high levels of NETs in many patients with COVID-19, where they may contribute to cytokine release and respiratory failure." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Neutrophil extracellular traps in COVID-19.", "journal": "JCI insight", "authors": "Zuo Y, Yalavarthi S, Shi H, Gockman K, Zuo M, Madison JA, Blair C, Weber A, Barnes BJ, Egeblad M, Woods RJ, Kanthi Y, Knight JS", "date": "2020-04-25", "evidence": [], "reference": [ { "id": "32329756", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32329756" } ] } ], "biomarker_canonical_id": "AN6380", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "c": "condition", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6435-1", "biomarker_component": [ { "biomarker": "increased OXLDL level", "assessed_biomarker_entity": { "recommended_name": "Oxidized low-density lipoprotein antibody", "synonyms": [] }, "assessed_biomarker_entity_id": "NCIt:C204113", "assessed_entity_type": "lipoprotein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "54238-1" } ], "evidence_source": [ { "id": "15533907", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/15533907", "evidence_list": [ { "evidence": "Higher levels of serum oxLDL may increase risk of colorectal cancer. Cases included both colon and rectal cancers. Risk for colon cancer only was increased with high serum oxLDL levels after adjusting for gender, age, study area, and potential confounders." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "risk" } ], "condition": { "id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_9256" }, "synonyms": [] }, "evidence_source": [ { "id": "15533907", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/15533907", "evidence_list": [ { "evidence": "Higher levels of serum oxLDL may increase risk of colorectal cancer. Cases included both colon and rectal cancers. Risk for colon cancer only was increased with high serum oxLDL levels after adjusting for gender, age, study area, and potential confounders." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Serum oxidized low-density lipoprotein levels and risk of colorectal cancer: a case-control study nested in the Japan Collaborative Cohort Study.", "journal": "Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology", "authors": "Suzuki K, Ito Y, Wakai K, Kawado M, Hashimoto S, Toyoshima H, Kojima M, Tokudome S, Hayakawa N, Watanabe Y, Tamakoshi K, Suzuki S, Ozasa K, Tamakoshi A, None None", "date": "2004-11-10", "evidence": [], "reference": [ { "id": "15533907", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/15533907" } ] } ], "biomarker_canonical_id": "AN6435", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "c": "condition", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6436-1", "biomarker_component": [ { "biomarker": "increased OXLDL level", "assessed_biomarker_entity": { "recommended_name": "Oxidized low-density lipoprotein", "synonyms": [] }, "assessed_biomarker_entity_id": "CHEBI:39026", "assessed_entity_type": "lipoprotein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "54238-1" } ], "evidence_source": [ { "id": "15533907", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/15533907", "evidence_list": [ { "evidence": "Higher levels of serum oxLDL may increase risk of colorectal cancer. Cases included both colon and rectal cancers. Risk for colon cancer only was increased with high serum oxLDL levels after adjusting for gender, age, study area, and potential confounders." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "risk" } ], "condition": { "id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_9256" }, "synonyms": [] }, "evidence_source": [ { "id": "15533907", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/15533907", "evidence_list": [ { "evidence": "Higher levels of serum oxLDL may increase risk of colorectal cancer. Cases included both colon and rectal cancers. Risk for colon cancer only was increased with high serum oxLDL levels after adjusting for gender, age, study area, and potential confounders." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Serum oxidized low-density lipoprotein levels and risk of colorectal cancer: a case-control study nested in the Japan Collaborative Cohort Study.", "journal": "Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology", "authors": "Suzuki K, Ito Y, Wakai K, Kawado M, Hashimoto S, Toyoshima H, Kojima M, Tokudome S, Hayakawa N, Watanabe Y, Tamakoshi K, Suzuki S, Ozasa K, Tamakoshi A, None None", "date": "2004-11-10", "evidence": [], "reference": [ { "id": "15533907", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/15533907" } ] } ], "biomarker_canonical_id": "AN6436", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "f": "frequency", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6437-1", "biomarker_component": [ { "biomarker": "increased NPPB level", "assessed_biomarker_entity": { "recommended_name": "N-terminal pro-brain natriuretic peptide", "synonyms": [ { "synonym": "Brain natriuretic factor prohormone" }, { "synonym": "preproBNP" }, { "synonym": "proBNP" }, { "synonym": "Gamma-brain natriuretic peptide" }, { "synonym": "Iso-ANP" } ] }, "assessed_biomarker_entity_id": "UPKB:P16860", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "71425-3" } ], "evidence_source": [ { "id": "20837460", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/20837460", "evidence_list": [ { "evidence": "Among 35 patients with lung cancer, 26 (74%) had elevated NT-proBNP (>/= 125 pg/mL), versus 9 (26%) with NT-proBNP < 125 pg/mL (P < .0001). By multivariate analysis, the presence of lung cancer was an independent risk factor for a level of NT-proBNP >/= 125 pg/mL (odds ratio, 7; 95% CI, 2.9-17; P < .0001). In our study, patients with lung cancer were 7 times more likely to have elevated NT-proBNP (>/= 125 pg/mL)." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "risk" } ], "condition": { "id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1324" }, "synonyms": [] }, "evidence_source": [ { "id": "20837460", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/20837460", "evidence_list": [ { "evidence": "Among 35 patients with lung cancer, 26 (74%) had elevated NT-proBNP (>/= 125 pg/mL), versus 9 (26%) with NT-proBNP < 125 pg/mL (P < .0001). By multivariate analysis, the presence of lung cancer was an independent risk factor for a level of NT-proBNP >/= 125 pg/mL (odds ratio, 7; 95% CI, 2.9-17; P < .0001). In our study, patients with lung cancer were 7 times more likely to have elevated NT-proBNP (>/= 125 pg/mL)." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "High N-terminal pro-B-type natriuretic peptide: a biomarker of lung cancer?", "journal": "Clinical lung cancer", "authors": "Aujollet N, Meyer M, Cailliod R, Combier F, Coignet Y, Campard S, Facy O, Bernard A, Girard C", "date": "2010-09-15", "evidence": [], "reference": [ { "id": "20837460", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/20837460" } ] } ], "biomarker_canonical_id": "AN6437", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "c": "condition", "f": 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"resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019-nCoV infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019 Novel Coronavirus (2019-nCoV)", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" } ] }, "evidence_source": [ { "id": "32434874", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32434874", "evidence_list": [ { "evidence": "This meta-analysis showed elevated NT-proBNP level was associated with increased mortality in COVID-19 pneumonia." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Elevated N-terminal pro-brain natriuretic peptide is associated with increased mortality in patients with COVID-19: systematic review and meta-analysis.", "journal": "Postgraduate medical journal", "authors": "Pranata R, Huang I, Lukito AA, Raharjo SB", "date": "2020-05-22", "evidence": [], "reference": [ { "id": "32434874", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32434874" } ] } ], "biomarker_canonical_id": "AN6437", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "c": "condition", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6438-1", "biomarker_component": [ { "biomarker": "increased RDW", "assessed_biomarker_entity": { "recommended_name": "Coefficient of RBC distribution width", "synonyms": [] }, "assessed_biomarker_entity_id": "NCIt:C64800", "assessed_entity_type": "cell", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": 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"https://pubmed.ncbi.nlm.nih.gov/32296824", "evidence_list": [ { "evidence": "We found that old age, and higher serum lactate dehydrogenase, C-reactive protein, the coefficient of variation of red blood cell distribution width, blood urea nitrogen, direct bilirubin, lower albumin, are associated with severe COVID-19." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "A Tool for Early Prediction of Severe Coronavirus Disease 2019 (COVID-19): A Multicenter Study Using the Risk Nomogram in Wuhan and Guangdong, China.", "journal": "Clinical infectious diseases : an official publication of the Infectious Diseases Society of America", "authors": "Gong J, Ou J, Qiu X, Jie Y, Chen Y, Yuan L, Cao J, Tan M, Xu W, Zheng F, Shi Y, Hu B", "date": "2020-04-17", "evidence": [], "reference": [ { "id": "32296824", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32296824" } ] } ], "biomarker_canonical_id": "AN6438", "score": 1, 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Performance of all 3 biomarkers is lower in patients with high risk for HCC. each marker had higher levels in patients with HCC compared to cirrhotic controls." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "19362088", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/19362088", "evidence_list": [ { "evidence": "AFP was more sensitive than DCP and AFP-L3 for the diagnosis of early and very early stage HCC." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] }, { "id": "12717392", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/12717392", "evidence_list": [ { "evidence": "DCP was more sensitive and specific than AFP for differentiating HCC from nonmalignant chronic liver disease. 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"best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Elevated Expression of Serum Endothelial Cell Adhesion Molecules in COVID-19 Patients.", "journal": "The Journal of infectious diseases", "authors": "Tong M, Jiang Y, Xia D, Xiong Y, Zheng Q, Chen F, Zou L, Xiao W, Zhu Y", "date": "2020-06-26", "evidence": [], "reference": [ { "id": "32582936", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32582936" } ] } ], "biomarker_canonical_id": "AN6466", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "f": "frequency", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6467-1", "biomarker_component": [ { "biomarker": "Increased HELLS level", 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"assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1324" }, "synonyms": [] }, "evidence_source": [ { "id": "32195055", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32195055", "evidence_list": [ { "evidence": "An improved prognosis was associated with increased Helicase, Lymphoid-Specific (HELLS) and decreased Intercellular adhesion molecule 1 (ICAM1) mRNA expression in lung cancer patients." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Identification and validation of HELLS (Helicase, Lymphoid-Specific) and ICAM1 (Intercellular adhesion molecule 1) as potential diagnostic biomarkers of lung cancer.", "journal": "PeerJ", "authors": "Zhu W, Li LL, Songyang Y, Shi Z, Li D", "date": "2020-03-21", "evidence": [], "reference": [ { "id": "32195055", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32195055" } ] } ], "biomarker_canonical_id": "AN6467", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "f": "frequency", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6468-1", "biomarker_component": [ { "biomarker": "decreased ICAM-1 level", "assessed_biomarker_entity": { "recommended_name": "Intercellular adhesion molecule 1", "synonyms": [ { "synonym": "ICAM-1" }, { "synonym": "Major group rhinovirus receptor" } ] }, "assessed_biomarker_entity_id": "UPKB:P05362", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "17174-4" } ], "evidence_source": [ { "id": "32195055", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32195055", "evidence_list": [ { "evidence": "Improved prognosis was associated with ‚Ķ decreased Intercellular adhesion molecule 1 (ICAM1) mRNA expression in lung cancer patients." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1324" }, "synonyms": [] }, "evidence_source": [ { "id": "32195055", 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"variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6469-2", "biomarker_component": [ { "biomarker": "increased AOC3 level", "assessed_biomarker_entity": { "recommended_name": "Vascular adhesion protein-1", "synonyms": [ { "synonym": "Copper amine oxidase" }, { "synonym": "HPAO" }, { "synonym": "Semicarbazide-sensitive amine oxidase" }, { "synonym": "SSAO" }, { "synonym": "Vascular adhesion protein 1" }, { "synonym": "VAP-1" } ] }, "assessed_biomarker_entity_id": "UPKB:Q16853", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "30160019", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30160019", "evidence_list": [ { "evidence": "VAP-1 is shown to be a biomarker that can predict invasive potential and clinical outcome in breast cancer." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "name": "breast cancer", "description": "A thoracic cancer that originates in the mammary gland.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, "synonyms": [ { "id": "DOID:1612", "name": "malignant tumor of the breast", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "breast tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "mammary cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "primary breast cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "mammary tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "malignant neoplasm of breast", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" } ] }, "evidence_source": [ { "id": "30160019", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30160019", "evidence_list": [ { "evidence": "VAP-1 is shown to be a biomarker that can predict invasive potential and clinical outcome in breast cancer." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Vascular adhesion protein-1 as indicator of breast cancer tumor aggressiveness and invasiveness.", "journal": "APMIS : acta pathologica, microbiologica, et immunologica Scandinavica", "authors": "Lai YC, Chang SJ, Kostoro J, Kwan AL, Chai CY", "date": "2018-08-31", "evidence": [], "reference": [ { "id": "30160019", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30160019" } ] } ], "biomarker_canonical_id": "AN6469", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "f": "frequency", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6470-1", "biomarker_component": [ { "biomarker": "decreased SELENOP level", "assessed_biomarker_entity": { "recommended_name": "Selenoprotein P", "synonyms": [ { "synonym": "SeP" } ] }, "assessed_biomarker_entity_id": "UPKB:P49908", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "32708526", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32708526", "evidence_list": [ { "evidence": "The Se status was significantly higher in samples from surviving COVID patients as compared with non-survivors (Se; 53.3 ¬± 16.2 vs. 40.8 ¬± 8.1 ¬µg/L, SELENOP; 3.3 ¬± 1.3 vs. 2.1 ¬± 0.9 mg/L), recovering with time in survivors while remaining low or even declining in non-survivors. We conclude that Se status analysis in COVID patients provides diagnostic information patients suffering from COVID-19 display a deficiency in the essential trace element Se in blood, along with low concentrations of the Se transporter SELENOP and low enzymatic activity of the secreted GPx3." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:0080600", "recommended_name": { "id": "DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, "synonyms": [ { "id": "DOID:0080600", "name": "SARS-CoV-2 infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan coronavirus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "COVID19", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan seafood market pneumonia virus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019-nCoV infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "2019 Novel Coronavirus (2019-nCoV)", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" } ] }, "evidence_source": [ { "id": "32708526", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32708526", "evidence_list": [ { "evidence": "The Se status was significantly higher in samples from surviving COVID patients as compared with non-survivors (Se; 53.3 ¬± 16.2 vs. 40.8 ¬± 8.1 ¬µg/L, SELENOP; 3.3 ¬± 1.3 vs. 2.1 ¬± 0.9 mg/L), recovering with time in survivors while remaining low or even declining in non-survivors. We conclude that Se status analysis in COVID patients provides diagnostic information patients suffering from COVID-19 display a deficiency in the essential trace element Se in blood, along with low concentrations of the Se transporter SELENOP and low enzymatic activity of the secreted GPx3." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Selenium Deficiency Is Associated with Mortality Risk from COVID-19.", "journal": "Nutrients", "authors": "Moghaddam A, Heller RA, Sun Q, Seelig J, Cherkezov A, Seibert L, Hackler J, Seemann P, Diegmann J, Pilz M, Bachmann M, Minich WB, Schomburg L", "date": "2020-07-28", "evidence": [], "reference": [ { "id": "32708526", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32708526" } ] } ], "biomarker_canonical_id": "AN6470", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6471-1", "biomarker_component": [ { "biomarker": "increased IL17A level", "assessed_biomarker_entity": { "recommended_name": "Interleukin-17A", "synonyms": [ { "synonym": "IL-17" }, { "synonym": "IL-17A" }, { "synonym": "Cytotoxic T-lymphocyte-associated antigen 8" }, { "synonym": "CTLA-8" } ] }, "assessed_biomarker_entity_id": "UPKB:Q16552", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "82334-4" } ], "evidence_source": [ { "id": "32576222", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32576222", "evidence_list": [ { "evidence": "Levels of VEGF-D, TNF-alpha, SCF, LIF, IL-2, IL-4, IL-6, IL-8, IL-10, IL-15, IL-17A, IL-18, IL-1 beta, and IFN-gamma were significantly higher in the critical group than in the severe group (Table 1)." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "monitoring" } ], "condition": { "id": "DOID:0080600", "recommended_name": { "id": "DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, "synonyms": [ { "id": "DOID:0080600", "name": "SARS-CoV-2 infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { "id": "DOID:0080600", "name": "Wuhan coronavirus infection", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_0080600" }, { 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AUC of HP, APOA1 and CEA were 0.929, 0.840 and 0.877, respectively." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Haptoglobin is a serological biomarker for adenocarcinoma lung cancer by using the ProteomeLab PF2D combined with mass spectrometry.", "journal": "American journal of cancer research", "authors": "Chang YK, Lai YH, Chu Y, Lee MC, Huang CY, Wu S", "date": "2016-09-21", "evidence": [], "reference": [ { "id": "27648369", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/27648369" } ] } ], "biomarker_canonical_id": "AN6476", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "c": "condition", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6477-1", "biomarker_component": [ { "biomarker": "increased ALCAM level", "assessed_biomarker_entity": { "recommended_name": "Activated leukocyte cell adhesion molecule", "synonyms": [ { "synonym": "Activated leukocyte cell adhesion molecule" } ] }, "assessed_biomarker_entity_id": "UPKB:Q13740", "assessed_entity_type": "protein", "specimen": [ { "name": "skin epidermis", "id": "UBERON:0001003", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0001003", "loinc_code": "" } ], "evidence_source": [ { "id": "26134500", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/26134500", "evidence_list": [ { "evidence": "High ALCAM expression in primary melanoma cells (IRS >/=8) is strongly correlated with unfavorable prognosis as compared with patients with lower ALCAM immunoreactivity in tumor compartment as regards cancer specific overall survival (CSOS) (P = 0.001) and disease free survival (DFS) (P < 0.001). High ALCAM expression in melanoma cells of the primary tumor can be used as a marker of negative outcome and may indicate a more invasive phenotype of cancer cells, which would require a more intensive therapeutic strategy." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0001003" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_4159" }, "synonyms": [ { "id": "DOID:4159", "name": "CA - skin cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_4159" }, { "id": "DOID:4159", "name": "malignant neoplasm of skin", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_4159" }, { "id": "DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_4159" } ] }, "evidence_source": [ { "id": "26134500", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/26134500", "evidence_list": [ { "evidence": "High ALCAM expression in primary melanoma cells (IRS >/=8) is strongly correlated with unfavorable prognosis as compared with patients with lower ALCAM immunoreactivity in tumor compartment as regards cancer specific overall survival (CSOS) (P = 0.001) and disease free survival (DFS) (P < 0.001). High ALCAM expression in melanoma cells of the primary tumor can be used as a marker of negative outcome and may indicate a more invasive phenotype of cancer cells, which would require a more intensive therapeutic strategy." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Prognostic significance of ALCAM (CD166/MEMD) expression in cutaneous melanoma patients.", "journal": "Diagnostic pathology", "authors": "Donizy P, Zietek M, Halon A, Leskiewicz M, Kozyra C, Matkowski R", "date": "2015-07-03", "evidence": [], "reference": [ { "id": "26134500", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/26134500" } ] } ], "biomarker_canonical_id": "AN6477", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "c": "condition", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6478-1", "biomarker_component": [ { "biomarker": "decreased BRMS1 level", "assessed_biomarker_entity": { "recommended_name": "Breast cancer metastasis suppressor 1", "synonyms": [] }, "assessed_biomarker_entity_id": "UPKB:Q9HCU9", "assessed_entity_type": "protein", "specimen": [ { "name": "skin epidermis", "id": "UBERON:0001003", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0001003", "loinc_code": "" } ], "evidence_source": [ { "id": "20935672", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/20935672", "evidence_list": [ { "evidence": "BRMS1 expression was significantly correlated with disease-specific 5-year survival of melanoma patients (P=0.007, log-rank test). Multivariate Cox regression analysis revealed that BRMS1 staining was an independent prognostic factor for melanoma patients (relative risk=0.51; confidence interval=0.29-0.91; P=0.022). BRMS1 expression was significantly decreased in metastatic melanoma compared with primary melanoma or dysplastic nevi (P=0.021 and 0.001, respectively, chi(2) test). BRMS1 may serve an important prognostic marker and therapeutic target for melanoma patients." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0001003" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_4159" }, "synonyms": [ { "id": "DOID:4159", "name": "CA - skin cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_4159" }, { "id": "DOID:4159", "name": "malignant neoplasm of skin", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_4159" }, { "id": "DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_4159" } ] }, "evidence_source": [ { "id": "20935672", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/20935672", "evidence_list": [ { "evidence": "BRMS1 expression was significantly correlated with disease-specific 5-year survival of melanoma patients (P=0.007, log-rank test). Multivariate Cox regression analysis revealed that BRMS1 staining was an independent prognostic factor for melanoma patients (relative risk=0.51; confidence interval=0.29-0.91; P=0.022). BRMS1 expression was significantly decreased in metastatic melanoma compared with primary melanoma or dysplastic nevi (P=0.021 and 0.001, respectively, chi(2) test). BRMS1 may serve an important prognostic marker and therapeutic target for melanoma patients." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Prognostic significance of BRMS1 expression in human melanoma and its role in tumor angiogenesis.", "journal": "Oncogene", "authors": "Li J, Cheng Y, Tai D, Martinka M, Welch DR, Li G", "date": "2010-10-12", "evidence": [], "reference": [ { "id": "20935672", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/20935672" } ] } ], "biomarker_canonical_id": "AN6478", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "f": "frequency", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6479-1", "biomarker_component": [ { "biomarker": "presence of methylation in DCC", "assessed_biomarker_entity": { "recommended_name": "DCC netrin receptor 1", "synonyms": [ { "synonym": "CRC18" }, { "synonym": "CRCR1" }, { "synonym": "HGPPS2" }, { "synonym": "IGDCC1" }, { "synonym": "MRMV1" }, { "synonym": "NTN1R1" } ] }, "assessed_biomarker_entity_id": "NCBI: 1630", "assessed_entity_type": "gene", "specimen": [ { "name": "oral cavity", "id": "UBERON:0000167", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000167", "loinc_code": "" } ], "evidence_source": [ { "id": "21558411", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/21558411", "evidence_list": [ { "evidence": "EDNRB, HOXA9, GATA4, NID2, KIF1A, DCC show differential methylation between cases and controls. Promoter methylation of KIF1A, NID2, and EDNRB had a moderate to substantial agreement with clinical diagnosis." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000167" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:11934", "recommended_name": { "id": "DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11934" }, "synonyms": [ { "id": "DOID:11934", "name": "head and neck neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11934" }, { "id": "DOID:11934", "name": "head/neck neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11934" }, { "id": "DOID:11934", "name": "head and neck tumours", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11934" }, { "id": "DOID:11934", "name": "tumor of head and neck", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11934" } ] }, "evidence_source": [ { "id": "21558411", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/21558411", "evidence_list": [ { "evidence": "EDNRB, HOXA9, GATA4, NID2, KIF1A, DCC show differential methylation between cases and controls. Promoter methylation of KIF1A, NID2, and EDNRB had a moderate to substantial agreement with clinical diagnosis." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "NID2 and HOXA9 promoter hypermethylation as biomarkers for prevention and early detection in oral cavity squamous cell carcinoma tissues and saliva.", "journal": "Cancer prevention research (Philadelphia, Pa.)", "authors": "Guerrero-Preston R, Soudry E, Acero J, Orera M, Moreno-López L, Macía-Colón G, Jaffe A, Berdasco M, Ili-Gangas C, Brebi-Mieville P, Fu Y, Engstrom C, Irizarry RA, Esteller M, Westra W, Koch W, Califano J, Sidransky D", "date": "2011-05-12", "evidence": [], "reference": [ { "id": "21558411", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/21558411" } ] } ], "biomarker_canonical_id": "AN6479", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "f": "frequency", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6480-1", "biomarker_component": [ { "biomarker": "decreased EDNRB level", "assessed_biomarker_entity": { "recommended_name": "Endothelin receptor type B", "synonyms": [ { "synonym": "ET-B" }, { "synonym": "ET-BR" }, { "synonym": "Endothelin receptor non-selective type" } ] }, "assessed_biomarker_entity_id": "UPKB:P24530", "assessed_entity_type": "protein", "specimen": [ { "name": "breast", "id": "UBERON:0000310", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000310", "loinc_code": "" } ], "evidence_source": [ { "id": "32934717", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32934717", "evidence_list": [ { "evidence": "EDNRB expression was low in TNBC samples (P<0.01). In conclusion, EDNRB was associated with a favorable prognosis in patients with TNBC, and may be used as a novel prognostic biomarker." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000310" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "name": "breast cancer", "description": "A thoracic cancer that originates in the mammary gland.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, "synonyms": [ { "id": "DOID:1612", "name": "malignant tumor of the breast", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "breast tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "mammary cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "primary breast cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "mammary tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "malignant neoplasm of breast", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" } ] }, "evidence_source": [ { "id": "32934717", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32934717", "evidence_list": [ { "evidence": "EDNRB expression was low in TNBC samples (P<0.01). In conclusion, EDNRB was associated with a favorable prognosis in patients with TNBC, and may be used as a novel prognostic biomarker." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Prognostic values of EDNRB in triple-negative breast cancer.", "journal": "Oncology letters", "authors": "Liu S, Zhang J, Zhu J, Jiao D, Liu Z", "date": "2020-09-17", "evidence": [], "reference": [ { "id": "32934717", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32934717" } ] } ], "biomarker_canonical_id": "AN6480", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6481-1", "biomarker_component": [ { "biomarker": "presence of promoter methylation in EDNRB", "assessed_biomarker_entity": { "recommended_name": "Endothelin receptor type B gene", "synonyms": [ { "synonym": "ABCDS" }, { "synonym": "ET-B" }, { "synonym": "ET-BR" }, { "synonym": "ETB" }, { "synonym": "ETB1" }, { "synonym": "ETBR" }, { "synonym": "ETRB" }, { "synonym": "HSCR" }, { "synonym": "HSCR2" }, { "synonym": "WS4A" } ] }, "assessed_biomarker_entity_id": "NCBI: 1910", "assessed_entity_type": "gene", "specimen": [ { "name": "oral cavity", "id": "UBERON:0000167", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000167", "loinc_code": "" } ], "evidence_source": [ { "id": "21558411", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/21558411", "evidence_list": [ { "evidence": "EDNRB, HOXA9, GATA4, NID2, KIF1A, DCC show differential methylation between cases and controls. Promoter methylation of KIF1A, NID2, and EDNRB had a moderate to substantial agreement with clinical diagnosis." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000167" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:11934", "recommended_name": { "id": "DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11934" }, "synonyms": [ { "id": "DOID:11934", "name": "head and neck neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11934" }, { "id": "DOID:11934", "name": "head/neck neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11934" }, { "id": "DOID:11934", "name": "head and neck tumours", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11934" }, { "id": "DOID:11934", "name": "tumor of head and neck", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11934" } ] }, "evidence_source": [ { "id": "21558411", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/21558411", "evidence_list": [ { "evidence": "EDNRB, HOXA9, GATA4, NID2, KIF1A, DCC show differential methylation between cases and controls. Promoter methylation of KIF1A, NID2, and EDNRB had a moderate to substantial agreement with clinical diagnosis." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "NID2 and HOXA9 promoter hypermethylation as biomarkers for prevention and early detection in oral cavity squamous cell carcinoma tissues and saliva.", "journal": "Cancer prevention research (Philadelphia, Pa.)", "authors": "Guerrero-Preston R, Soudry E, Acero J, Orera M, Moreno-López L, Macía-Colón G, Jaffe A, Berdasco M, Ili-Gangas C, Brebi-Mieville P, Fu Y, Engstrom C, Irizarry RA, Esteller M, Westra W, Koch W, Califano J, Sidransky D", "date": "2011-05-12", "evidence": [], "reference": [ { "id": "21558411", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/21558411" } ] } ], "biomarker_canonical_id": "AN6481", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "c": "condition", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6482-1", "biomarker_component": [ { "biomarker": "decreased GATA-4 level", "assessed_biomarker_entity": { "recommended_name": "Transcription factor GATA-4", "synonyms": [ { "synonym": "GATA-binding factor 4" } ] }, "assessed_biomarker_entity_id": "UPKB:P43694", "assessed_entity_type": "protein", "specimen": [ { "name": "breast", "id": "UBERON:0000310", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000310", "loinc_code": "" } ], "evidence_source": [ { "id": "30187949", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30187949", "evidence_list": [ { "evidence": "GATA4 overexpression decreased viability, invasion, migration, and epithelial-to-mesenchymal transition of MB-231 and BT549 cells, and markedly induced cell cycle arrest and apoptosis. Our findings suggest that GATA4 is a potential prognostic biomarker and gene therapeutic target for human BrCa." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000310" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "name": "breast cancer", "description": "A thoracic cancer that originates in the mammary gland.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, "synonyms": [ { "id": "DOID:1612", "name": "malignant tumor of the breast", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "breast tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "mammary cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "primary breast cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "mammary tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "malignant neoplasm of breast", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" } ] }, "evidence_source": [ { "id": "30187949", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30187949", "evidence_list": [ { "evidence": "GATA4 overexpression decreased viability, invasion, migration, and epithelial-to-mesenchymal transition of MB-231 and BT549 cells, and markedly induced cell cycle arrest and apoptosis. 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Promoter methylation of KIF1A, NID2, and EDNRB had a moderate to substantial agreement with clinical diagnosis." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "NID2 and HOXA9 promoter hypermethylation as biomarkers for prevention and early detection in oral cavity squamous cell carcinoma tissues and saliva.", "journal": "Cancer prevention research (Philadelphia, Pa.)", "authors": "Guerrero-Preston R, Soudry E, Acero J, Orera M, Moreno-López L, Macía-Colón G, Jaffe A, Berdasco M, Ili-Gangas C, Brebi-Mieville P, Fu Y, Engstrom C, Irizarry RA, Esteller M, Westra W, Koch W, Califano J, Sidransky D", "date": "2011-05-12", "evidence": [], "reference": [ { "id": "21558411", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/21558411" } ] } ], "biomarker_canonical_id": "AN6487", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "c": "condition", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6488-1", "biomarker_component": [ { "biomarker": "increased NID2 level", "assessed_biomarker_entity": { "recommended_name": "Nidogen-2", "synonyms": [ { "synonym": "NID-2" }, { "synonym": "Osteonidogen" } ] }, "assessed_biomarker_entity_id": "UPKB:Q14112", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "29278876", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/29278876", "evidence_list": [ { "evidence": "The serum NID2 levels in ESCC patients (median 24.4 ug/L) are significantly higher (p= 4.3e-09) than that of the healthy controls (median 15.85 ug/L). 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In conclusion, we show that detecting the elevation of serum NID2 levels has potential diagnostic and prognostic value for ESCC patients." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Elevated levels of serum nidogen-2 in esophageal squamous cell carcinoma.", "journal": "Cancer biomarkers : section A of Disease markers", "authors": "Chai AWY, Cheung AKL, Dai W, Ko JMY, Lee NPY, Chan KT, Law SY, Lung ML", "date": "2017-12-28", "evidence": [], "reference": [ { "id": "29278876", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/29278876" } ] } ], "biomarker_canonical_id": "AN6488", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "f": "frequency", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6489-1", "biomarker_component": [ { "biomarker": "presence of promoter methylation NID2", "assessed_biomarker_entity": { "recommended_name": "Nidogen-2 gene", "synonyms": [ { "synonym": "NID-2" } ] }, "assessed_biomarker_entity_id": "NCBI: 22795", "assessed_entity_type": "gene", "specimen": [ { "name": "oral cavity", "id": "UBERON:0000167", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000167", "loinc_code": "" } ], "evidence_source": [ { "id": "21558411", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/21558411", "evidence_list": [ { "evidence": "EDNRB, HOXA9, GATA4, NID2, KIF1A, DCC show differential methylation between cases and controls. 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Thus, we demonstrated that miR-498 suppresses the growth and metastasis of liver cancer cells, partly at least, by directly targeting ZEB2, suggesting that miR-498 may serve as a potential biomarker for the diagnosis and therapy of liver cancer." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "miR‑498 inhibits the growth and metastasis of liver cancer by targeting ZEB2.", "journal": "Oncology reports", "authors": "Zhang X, Xu X, Ge G, Zang X, Shao M, Zou S, Zhang Y, Mao Z, Zhang J, Mao F, Qian H, Xu W", "date": "2018-12-29", "evidence": [], "reference": [ { "id": "30592286", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30592286" } ] } ], "biomarker_canonical_id": "AN6490", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "f": "frequency", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6491-1", "biomarker_component": [ { "biomarker": "decreased OGDHL level", "assessed_biomarker_entity": { "recommended_name": "Oxoglutarate dehydrogenase-like", "synonyms": [ { "synonym": "AKGDH" }, { "synonym": "E1k" }, { "synonym": "E1o" }, { "synonym": "KGD1" }, { "synonym": "OGDC" }, { "synonym": "OGDH-E1" }, { "synonym": "OGDH2" }, { "synonym": "OGDHD" } ] }, "assessed_biomarker_entity_id": "NCBI: 4967", "assessed_entity_type": "gene", "specimen": [ { "name": "liver", "id": "UBERON:0002107", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0002107", "loinc_code": "" } ], "evidence_source": [ { "id": "31781311", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31781311", "evidence_list": [ { "evidence": "OGDHL had lower expression in cancerous liver tissues than noncancerous adjacent tissues, and low expression correlated with more advanced patient age, histologic grade, stage, T classification, and poor survival. Survival analysis showed that patients with lower OGDHL levels had shorter overall survival (OS), and subgroup analysis indicated this relationship also held for patients with grade G1/G2, stage I/II, T3, N0, and M0 cancers. In addition, patients with lower OGDHL levels had shorter relapse-free survival, and subgroup analysis indicated this relationship also held for patients with grade G1/G2, stage III/IV, T1, T3, N0, and M1 cancers. Patients with lower OGDHL expression had shorter OS and relapse-free survival. Multivariate Cox regression indicated that low OGDHL expression was an independent risk factor for poor prognosis." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0002107" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:3571", "recommended_name": { "id": "DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, "synonyms": [ { "id": "DOID:3571", "name": "resectable malignant neoplasm of the liver", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "primary liver cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "Resectable malignant neoplasm of Liver", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "neoplasm of liver", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "malignant tumor of liver", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "malignant neoplasm of liver, primary", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "Ca liver - primary", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "primary malignant neoplasm of liver", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "hepatic neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "hepatic cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "malignant hepato-biliary neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "malignant neoplasm of liver", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" } ] }, "evidence_source": [ { "id": "31781311", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31781311", "evidence_list": [ { "evidence": "OGDHL had lower expression in cancerous liver tissues than noncancerous adjacent tissues, and low expression correlated with more advanced patient age, histologic grade, stage, T classification, and poor survival. Survival analysis showed that patients with lower OGDHL levels had shorter overall survival (OS), and subgroup analysis indicated this relationship also held for patients with grade G1/G2, stage I/II, T3, N0, and M0 cancers. In addition, patients with lower OGDHL levels had shorter relapse-free survival, and subgroup analysis indicated this relationship also held for patients with grade G1/G2, stage III/IV, T1, T3, N0, and M1 cancers. Patients with lower OGDHL expression had shorter OS and relapse-free survival. Multivariate Cox regression indicated that low OGDHL expression was an independent risk factor for poor prognosis." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "", "journal": "Disease markers", "authors": "Jiao Y, Li Y, Fu Z, Hou L, Chen Q, Cai Y, Jiang P, He M, Yang Z", "date": "2019-11-30", "evidence": [], "reference": [ { "id": "31781311", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31781311" } ] } ], "biomarker_canonical_id": "AN6491", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "w": "weight", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6492-1", "biomarker_component": [ { "biomarker": "increased HSP90AA1 level", "assessed_biomarker_entity": { "recommended_name": "Heat shock protein 90 alpha", "synonyms": [ { "synonym": "Heat shock 86 kDa" }, { "synonym": "HSP 86" }, { "synonym": "HSP86" }, { "synonym": "Lipopolysaccharide-associated protein 2" }, { "synonym": "LAP-2" }, { "synonym": "LPS-associated protein 2" }, { "synonym": "Renal carcinoma antigen NY-REN-38" } ] }, "assessed_biomarker_entity_id": "UPKB:P07900", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "28939487", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/28939487", "evidence_list": [ { "evidence": "Diagnostic performance of plasma Hsp90a was evaluated by the calculated sensitivity, specificity, and area under the receiver operating characteristic curve (AUC). ROC curve showed plasma Hsp90a can discriminating liver cancer with a sensitivity of 92.7% and specificity of 91.3% from non-liver cancer control." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:3571", "recommended_name": { "id": "DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, "synonyms": [ { "id": "DOID:3571", "name": "resectable malignant neoplasm of the liver", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "primary liver cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "Resectable malignant neoplasm of Liver", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "neoplasm of liver", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "malignant tumor of liver", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "malignant neoplasm of liver, primary", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "Ca liver - primary", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "primary malignant neoplasm of liver", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "hepatic neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "hepatic cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "malignant hepato-biliary neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "malignant neoplasm of liver", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" } ] }, "evidence_source": [ { "id": "28939487", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/28939487", "evidence_list": [ { "evidence": "Diagnostic performance of plasma Hsp90a was evaluated by the calculated sensitivity, specificity, and area under the receiver operating characteristic curve (AUC). ROC curve showed plasma Hsp90a can discriminating liver cancer with a sensitivity of 92.7% and specificity of 91.3% from non-liver cancer control." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Plasma Heat Shock Protein 90alpha as a Biomarker for the Diagnosis of Liver Cancer: An Official, Large-scale, and Multicenter Clinical Trial.", "journal": "EBioMedicine", "authors": "Fu Y, Xu X, Huang D, Cui D, Liu L, Liu J, He Z, Liu J, Zheng S, Luo Y", "date": "2017-09-25", "evidence": [], "reference": [ { "id": "28939487", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/28939487" } ] } ], "biomarker_canonical_id": "AN6492", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6493-1", "biomarker_component": [ { "biomarker": "decreased SLC25A11 level", "assessed_biomarker_entity": { "recommended_name": "Mitochondrial 2-oxoglutarate/malate carrier protein", "synonyms": [ { "synonym": "OGC" }, { "synonym": "PGL6" }, { "synonym": "PPGL6" }, { "synonym": "SLC20A4" } ] }, "assessed_biomarker_entity_id": "NCBI: 8402", "assessed_entity_type": "gene", "specimen": [ { "name": "liver", "id": "UBERON:0002107", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0002107", "loinc_code": "" } ], "evidence_source": [ { "id": "32555317", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32555317", "evidence_list": [ { "evidence": "Liver cancer patients with low SLC25A11 expression had shorter OS and RFS than patients with high SLC25A11 expression. Multivariate analysis showed that the expression of SLC25A11 was an independent predictor of RFS and OS. In conclusion, this study identified that SLC25A11 serves as a new prognostic marker for liver cancer." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0002107" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:3571", "recommended_name": { "id": "DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, "synonyms": [ { "id": "DOID:3571", "name": "resectable malignant neoplasm of the liver", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "primary liver cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "Resectable malignant neoplasm of Liver", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "neoplasm of liver", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "malignant tumor of liver", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "malignant neoplasm of liver, primary", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "Ca liver - primary", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "primary malignant neoplasm of liver", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "hepatic neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "hepatic cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "malignant hepato-biliary neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "malignant neoplasm of liver", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" } ] }, "evidence_source": [ { "id": "32555317", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32555317", "evidence_list": [ { "evidence": "Liver cancer patients with low SLC25A11 expression had shorter OS and RFS than patients with high SLC25A11 expression. Multivariate analysis showed that the expression of SLC25A11 was an independent predictor of RFS and OS. In conclusion, this study identified that SLC25A11 serves as a new prognostic marker for liver cancer." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "SLC25A11 serves as a novel prognostic biomarker in liver cancer.", "journal": "Scientific reports", "authors": "Pan G, Wang R, Jia S, Li Y, Jiao Y, Liu N", "date": "2020-06-20", "evidence": [], "reference": [ { "id": "32555317", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32555317" } ] } ], "biomarker_canonical_id": "AN6493", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "w": "weight", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6494-1", "biomarker_component": [ { "biomarker": "increased DCK level", "assessed_biomarker_entity": { "recommended_name": "Deoxycytidine kinase", "synonyms": [] }, "assessed_biomarker_entity_id": "NCBI: 1633", "assessed_entity_type": "gene", "specimen": [ { "name": "liver", "id": "UBERON:0002107", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0002107", "loinc_code": "" } ], "evidence_source": [ { "id": "32588770", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32588770", "evidence_list": [ { "evidence": "The deoxycytidine kinase messenger RNA level significantly upregulated in patients with liver cancer compared to normal liver samples. All the above findings suggested that increased expression of deoxycytidine kinase was significantly related to unfavorable prognosis in patients with liver cancer. Deoxycytidine kinase is correlated with immune infiltrating levels, including those of B cells, macrophages, neutrophils, and dendritic cells in patients with liver cancer. The survival curves revealed that in patients with liver cancer, the high expression level of DCK (RNA-SeqID:1633) indicated worse prognosis. high expression of DCK resulted in shorter OS (HR = 1.90, 95% CI = 1.32-2.72, P value = .00043) and RFS (HR = 1.53, 95% CI = 1.10-2.13, P value = .011)." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0002107" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:3571", "recommended_name": { "id": "DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, "synonyms": [ { "id": "DOID:3571", "name": "resectable malignant neoplasm of the liver", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "primary liver cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "Resectable malignant neoplasm of Liver", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "neoplasm of liver", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "malignant tumor of liver", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "malignant neoplasm of liver, primary", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "Ca liver - primary", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "primary malignant neoplasm of liver", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "hepatic neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "hepatic cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "malignant hepato-biliary neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "malignant neoplasm of liver", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" } ] }, "evidence_source": [ { "id": "32588770", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32588770", "evidence_list": [ { "evidence": "The deoxycytidine kinase messenger RNA level significantly upregulated in patients with liver cancer compared to normal liver samples. All the above findings suggested that increased expression of deoxycytidine kinase was significantly related to unfavorable prognosis in patients with liver cancer. Deoxycytidine kinase is correlated with immune infiltrating levels, including those of B cells, macrophages, neutrophils, and dendritic cells in patients with liver cancer. The survival curves revealed that in patients with liver cancer, the high expression level of DCK (RNA-SeqID:1633) indicated worse prognosis. high expression of DCK resulted in shorter OS (HR = 1.90, 95% CI = 1.32-2.72, P value = .00043) and RFS (HR = 1.53, 95% CI = 1.10-2.13, P value = .011)." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "DCK is an Unfavorable Prognostic Biomarker and Correlated With Immune Infiltrates in Liver Cancer.", "journal": "Technology in cancer research & treatment", "authors": "Hu SF, Lin X, Xu LP, Chen HG, Guo JF, Jin L", "date": "2020-06-27", "evidence": [], "reference": [ { "id": "32588770", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32588770" } ] } ], "biomarker_canonical_id": "AN6494", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6495-1", "biomarker_component": [ { "biomarker": "increased H2AX level", "assessed_biomarker_entity": { "recommended_name": "Histone H2AX", "synonyms": [ { "synonym": "H2a/x" }, { "synonym": "Histone H2A.X" } ] }, "assessed_biomarker_entity_id": "UPKB:P16104", "assessed_entity_type": "protein", "specimen": [ { "name": "breast", "id": "UBERON:0000310", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000310", "loinc_code": "" } ], "evidence_source": [ { "id": "31552812", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31552812", "evidence_list": [ { "evidence": "Greater tumor size, higher grade, and the number of affected lymph nodes are significantly associated with greater values of gamma-H2AX. Higher values of estrogen receptor and progesterone receptor are significantly associated with lower gamma-H2AX values. In conclusion, a positive association between gamma-H2AX expression and infaust histopathological parameters was observed." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000310" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "name": "breast cancer", "description": "A thoracic cancer that originates in the mammary gland.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, "synonyms": [ { "id": "DOID:1612", "name": "malignant tumor of the breast", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "breast tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "mammary cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "primary breast cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "mammary tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "malignant neoplasm of breast", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" } ] }, "evidence_source": [ { "id": "31552812", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31552812", "evidence_list": [ { "evidence": "Greater tumor size, higher grade, and the number of affected lymph nodes are significantly associated with greater values of gamma-H2AX. Higher values of estrogen receptor and progesterone receptor are significantly associated with lower gamma-H2AX values. In conclusion, a positive association between gamma-H2AX expression and infaust histopathological parameters was observed." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "gamma-H2AX: A potential biomarker in breast cancer.", "journal": "Tumour biology : the journal of the International Society for Oncodevelopmental Biology and Medicine", "authors": "Varvara PV, Karaolanis G, Valavanis C, Stanc G, Tzaida O, Trihia H, Patapis P, Dimitroulis D, Perrea D", "date": "2019-09-26", "evidence": [], "reference": [ { "id": "31552812", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31552812" } ] } ], "biomarker_canonical_id": "AN6495", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6496-1", "biomarker_component": [ { "biomarker": "increased CTDNA level", "assessed_biomarker_entity": { "recommended_name": "Circulating tumor-derived DNA", "synonyms": [] }, "assessed_biomarker_entity_id": "NCIt:C113243", "assessed_entity_type": "DNA", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "31070691", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31070691", "evidence_list": [ { "evidence": "During surveillance after definitive therapy, ctDNA-positive patients were more than 40 times more likely to experience disease recurrence than ctDNA negative patients (HR, 43.5; 95% CI, 9.8-193.5 P < .001). In all multivariate analyses, ctDNA status was independently associated with relapse after adjusting for known clinicopathologic risk factors. Circulating tumor DNA analysis can potentially change the postoperative management of CRC by enabling risk stratification, ACT monitoring, and early relapse detection." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "monitoring" } ], "condition": { "id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_9256" }, "synonyms": [] }, "evidence_source": [ { "id": "31070691", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31070691", "evidence_list": [ { "evidence": "During surveillance after definitive therapy, ctDNA-positive patients were more than 40 times more likely to experience disease recurrence than ctDNA negative patients (HR, 43.5; 95% CI, 9.8-193.5 P < .001). In all multivariate analyses, ctDNA status was independently associated with relapse after adjusting for known clinicopathologic risk factors. Circulating tumor DNA analysis can potentially change the postoperative management of CRC by enabling risk stratification, ACT monitoring, and early relapse detection." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Analysis of Plasma Cell-Free DNA by Ultradeep Sequencing in Patients With Stages I to III Colorectal Cancer.", "journal": "JAMA oncology", "authors": "Reinert T, Henriksen TV, Christensen E, Sharma S, Salari R, Sethi H, Knudsen M, Nordentoft I, Wu HT, Tin AS, Heilskov Rasmussen M, Vang S, Shchegrova S, Frydendahl Boll Johansen A, Srinivasan R, Assaf Z, Balcioglu M, Olson A, Dashner S, Hafez D, Navarro S, Goel S, Rabinowitz M, Billings P, Sigurjonsson S, Dyrskjøt L, Swenerton R, Aleshin A, Laurberg S, Husted Madsen A, Kannerup AS, Stribolt K, Palmelund Krag S, Iversen LH, Gotschalck Sunesen K, Lin CJ, Zimmermann BG, Lindbjerg Andersen C", "date": "2019-05-10", "evidence": [], "reference": [ { "id": "31070691", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31070691" } ] } ], "biomarker_canonical_id": "AN6496", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "c": "condition", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6497-1", "biomarker_component": [ { "biomarker": "increased of TRAF2 level", "assessed_biomarker_entity": { "recommended_name": "Tumor necrosis factor receptor-associated factor 2", "synonyms": [ { "synonym": "E3 ubiquitin-protein ligase TRAF2" }, { "synonym": "RING-type E3 ubiquitin transferase TRAF2" }, { "synonym": "Tumor necrosis factor type 2 receptor-associated protein 3" } ] }, "assessed_biomarker_entity_id": "UPKB:Q12933", "assessed_entity_type": "protein", "specimen": [ { "name": "prostate gland", "id": "UBERON:0002367", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0002367", "loinc_code": "" } ], "evidence_source": [ { "id": "28855498", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/28855498", "evidence_list": [ { "evidence": "We found that TRAF2 was significantly upregulated in prostate cancer compared with normal prostate samples (P<0.001). TRAF2 high expression was associated with poorer recurrence-free survival in prostate cancer patients (P=0.013). TRAF2 was found to be a valuable independent prognostic factor for predicting recurrence-free survival (P=0.026). TRAF2 could be a novel prognostic biomarker for predicting recurrence-free survival in patients with prostate cancer, which might be associated with the effects of TRAF2 in regulating TRAIL-induced apoptosis in prostate cancer cells via c-Flip/Caspase-8 signaling." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0002367" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, "synonyms": [ { "id": "DOID:10283", "name": "prostate neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "NGP - new growth of prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "tumor of the prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostate cancer, familial", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostatic neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "malignant tumor of the prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "hereditary prostate cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostatic cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" } ] }, "evidence_source": [ { "id": "28855498", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/28855498", "evidence_list": [ { "evidence": "We found that TRAF2 was significantly upregulated in prostate cancer compared with normal prostate samples (P<0.001). TRAF2 high expression was associated with poorer recurrence-free survival in prostate cancer patients (P=0.013). TRAF2 was found to be a valuable independent prognostic factor for predicting recurrence-free survival (P=0.026). TRAF2 could be a novel prognostic biomarker for predicting recurrence-free survival in patients with prostate cancer, which might be associated with the effects of TRAF2 in regulating TRAIL-induced apoptosis in prostate cancer cells via c-Flip/Caspase-8 signaling." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "TRAF2 is a Valuable Prognostic Biomarker in Patients with Prostate Cancer.", "journal": "Medical science monitor : international medical journal of experimental and clinical research", "authors": "Wei B, Liang J, Hu J, Mi Y, Ruan J, Zhang J, Wang Z, Hu Q, Jiang H, Ding Q", "date": "2017-09-01", "evidence": [], "reference": [ { "id": "28855498", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/28855498" } ] } ], "biomarker_canonical_id": "AN6497", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6498-1", "biomarker_component": [ { "biomarker": "decreased MIR-214 level", "assessed_biomarker_entity": { "recommended_name": "miRNA-214", "synonyms": [] }, "assessed_biomarker_entity_id": "MRB:MI0000290", "assessed_entity_type": "RNA", "specimen": [ { "name": "urine", "id": "UBERON:0001088", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0001088", "loinc_code": "" } ], "evidence_source": [ { "id": "25975233", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/25975233", "evidence_list": [ { "evidence": "Underexpressed extracellular miR-214 in urine was significantly associated with higher tumor stage, higher lymph node status, higher grade, age and history of non-muscle-invasive bladder cancer (NMIBC). Urinary cell-free miR-214 is a hopeful biomarker for tumor stratification, early diagnosis and prognostic assessment of bladder cancer." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0001088" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11054" }, "synonyms": [ { "id": "DOID:11054", "name": "tumor of the bladder", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11054" }, { "id": "DOID:11054", "name": "bladder cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11054" } ] }, "evidence_source": [ { "id": "25975233", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/25975233", "evidence_list": [ { "evidence": "Underexpressed extracellular miR-214 in urine was significantly associated with higher tumor stage, higher lymph node status, higher grade, age and history of non-muscle-invasive bladder cancer (NMIBC). Urinary cell-free miR-214 is a hopeful biomarker for tumor stratification, early diagnosis and prognostic assessment of bladder cancer." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Downregulation of urinary cell-free microRNA-214 as a diagnostic and prognostic biomarker in bladder cancer.", "journal": "Journal of surgical oncology", "authors": "Wang J, Zhang X, Wang L, Dong Z, Du L, Yang Y, Guo Y, Wang C", "date": "2015-05-16", "evidence": [], "reference": [ { "id": "25975233", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/25975233" } ] } ], "biomarker_canonical_id": "AN6498", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6499-1", "biomarker_component": [ { "biomarker": "decreased NDRG2 level", "assessed_biomarker_entity": { "recommended_name": "N-myc downstream-regulated gene 2", "synonyms": [ { "synonym": "N-myc downstream-regulated gene 2 protein" }, { "synonym": "Protein Syld709613" } ] }, "assessed_biomarker_entity_id": "UPKB:Q9UN36", "assessed_entity_type": "protein", "specimen": [ { "name": "urine", "id": "UBERON:0001088", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0001088", "loinc_code": "" } ], "evidence_source": [ { "id": "28953854", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/28953854", "evidence_list": [ { "evidence": "The relative NDRG2 expression were significantly downregulated both at mRNA and protein levels in urine of patients with bladder cancer and in cell lines, and its low expression was distinctively correlated with tumor grade and stage. NDRG2 was decreased in patients with bladder cancer and might be involved in the progression of this malignancy. Moreover, NDRG2 could be a potential independent diagnostic biomarker for bladder cancer." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0001088" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11054" }, "synonyms": [ { "id": "DOID:11054", "name": "tumor of the bladder", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11054" }, { "id": "DOID:11054", "name": "bladder cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11054" } ] }, "evidence_source": [ { "id": "28953854", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/28953854", "evidence_list": [ { "evidence": "The relative NDRG2 expression were significantly downregulated both at mRNA and protein levels in urine of patients with bladder cancer and in cell lines, and its low expression was distinctively correlated with tumor grade and stage. NDRG2 was decreased in patients with bladder cancer and might be involved in the progression of this malignancy. Moreover, NDRG2 could be a potential independent diagnostic biomarker for bladder cancer." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Expression of N-Myc Downstream-Regulated Gene 2 in Bladder Cancer and Its Potential Utility as a Urinary Diagnostic Biomarker.", "journal": "Medical science monitor : international medical journal of experimental and clinical research", "authors": "Zhang M, Ren B, Li Z, Niu W, Wang Y", "date": "2017-09-28", "evidence": [], "reference": [ { "id": "28953854", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/28953854" } ] } ], "biomarker_canonical_id": "AN6499", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "f": "frequency", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6500-1", "biomarker_component": [ { "biomarker": "increased FCN3 level", "assessed_biomarker_entity": { "recommended_name": "Ficolin-3", "synonyms": [ { "synonym": "Collagen/fibrinogen domain-containing lectin 3 p35" }, { "synonym": "Collagen/fibrinogen domain-containing protein 3" }, { "synonym": "Hakata antigen" } ] }, "assessed_biomarker_entity_id": "UPKB:O75636", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "31373851", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31373851", "evidence_list": [ { "evidence": "The serum ficolin-3 level in the esophageal squamous cell carcinoma (ESCC) group was significantly higher than in the esophageal adenocarcinoma (EAC) group (19.59 ¬± 4.35 ng/mL vs. 18.39 ¬± 5.42 ng/mL, p < 0.01). Serum ficolin-3 levels were identified as an independent prognostic biomarker for DSS and OS in Chinese patients with EC, especially EAC." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, "synonyms": [ { "id": "DOID:5041", "name": "Ca lower third oesophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant tumor of abdominal esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "Ca middle third oesophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant neoplasm of upper third esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "esophagus cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" } ] }, "evidence_source": [ { "id": "31373851", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31373851", "evidence_list": [ { "evidence": "The serum ficolin-3 level in the esophageal squamous cell carcinoma (ESCC) group was significantly higher than in the esophageal adenocarcinoma (EAC) group (19.59 ¬± 4.35 ng/mL vs. 18.39 ¬± 5.42 ng/mL, p < 0.01). Serum ficolin-3 levels were identified as an independent prognostic biomarker for DSS and OS in Chinese patients with EC, especially EAC." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Evaluation of Ficolin-3 as a Potential Prognostic Serum Biomarker in Chinese Patients with Esophageal Cancer.", "journal": "Genetic testing and molecular biomarkers", "authors": "Li Q, Lin Y", "date": "2019-08-03", "evidence": [], "reference": [ { "id": "31373851", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31373851" } ] } ], "biomarker_canonical_id": "AN6500", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "c": "condition", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6501-1", "biomarker_component": [ { "biomarker": "increased CHI3L1 level", "assessed_biomarker_entity": { "recommended_name": "Chitinase-3-like protein 1", "synonyms": [ { "synonym": "39 kDa synovial protein" }, { "synonym": "Cartilage glycoprotein 39" }, { "synonym": "CGP-39" }, { "synonym": "GP-39" }, { "synonym": "hCGP-39" }, { "synonym": "YKL-40" } ] }, "assessed_biomarker_entity_id": "UPKB:P36222", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "32162865", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32162865", "evidence_list": [ { "evidence": "Plasma YKL-40 levels were significantly higher in patients with lymph node metastasis than those that were non-metastatic (p = 0.005). This study indicated that YKL-40 may be a biomarker for esophageal cancer and potential biomarker for identification of invasive esophageal cancer." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, "synonyms": [ { "id": "DOID:5041", "name": "Ca lower third oesophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant tumor of abdominal esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "Ca middle third oesophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant neoplasm of upper third esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "esophagus cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" } ] }, "evidence_source": [ { "id": "32162865", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32162865", "evidence_list": [ { "evidence": "Plasma YKL-40 levels were significantly higher in patients with lymph node metastasis than those that were non-metastatic (p = 0.005). This study indicated that YKL-40 may be a biomarker for esophageal cancer and potential biomarker for identification of invasive esophageal cancer." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Plasma YKL-40: a Potential Biomarker for Tumor Invasion in Esophageal Cancer.", "journal": "Clinical laboratory", "authors": "Huang R, Yao J, Ding X, Liu J, Fan C, Duan H, Ye H", "date": "2020-03-13", "evidence": [], "reference": [ { "id": "32162865", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32162865" } ] } ], "biomarker_canonical_id": "AN6501", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6501-2", "biomarker_component": [ { "biomarker": "increased CHI3L1 level", "assessed_biomarker_entity": { "recommended_name": "Chitinase-3-like protein 1", "synonyms": [ { "synonym": "39 kDa synovial protein" }, { "synonym": "Cartilage glycoprotein 39" }, { "synonym": "CGP-39" }, { "synonym": "GP-39" }, { "synonym": "hCGP-39" }, { "synonym": "YKL-40" } ] }, "assessed_biomarker_entity_id": "UPKB:P36222", "assessed_entity_type": "protein", "specimen": [ { "name": "thyroid gland", "id": "UBERON:0002046", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0002046", "loinc_code": "" } ], "evidence_source": [ { "id": "32613636", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32613636", "evidence_list": [ { "evidence": "Here, we investigated the prognostic significance of CHI3L1 expression in thyroid neoplasms and examined the potential oncogenic roles. Compared with normal thyroid tissue and benign thyroid lesions that had low or no detectable CHI3L1 expression, CHI3L1 was overexpressed in both differentiated and undifferentiated thyroid cancer." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0002046" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:1781", "recommended_name": { "id": "DOID:1781", "name": "thyroid gland cancer", "description": "An endocrine gland cancer located in the thryoid gland located in the neck below the thyroid cartilage.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1781" }, "synonyms": [ { "id": "DOID:1781", "name": "neoplasm of thyroid gland", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1781" }, { "id": "DOID:1781", "name": "thyroid neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1781" }, { "id": "DOID:1781", "name": "thyroid gland cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1781" }, { "id": "DOID:1781", "name": "malignant tumour of thyroid gland", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1781" }, { "id": "DOID:1781", "name": "Thyroid gland neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1781" }, { "id": "DOID:1781", "name": "malignant neoplasm of thyroid gland", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1781" } ] }, "evidence_source": [ { "id": "32613636", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32613636", "evidence_list": [ { "evidence": "Here, we investigated the prognostic significance of CHI3L1 expression in thyroid neoplasms and examined the potential oncogenic roles. Compared with normal thyroid tissue and benign thyroid lesions that had low or no detectable CHI3L1 expression, CHI3L1 was overexpressed in both differentiated and undifferentiated thyroid cancer." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Overexpression of chitinase-3-like protein 1 is associated with structural recurrence in patients with differentiated thyroid cancer.", "journal": "The Journal of pathology", "authors": "Cheng SP, Lee JJ, Chang YC, Lin CH, Li YS, Liu CL", "date": "2020-07-03", "evidence": [], "reference": [ { "id": "32613636", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32613636" } ] } ], "biomarker_canonical_id": "AN6501", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "f": "frequency", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6502-1", "biomarker_component": [ { "biomarker": "decreased P4HA1 level", "assessed_biomarker_entity": { "recommended_name": "Prolyl 4-hydroxylase subunit alpha 1", "synonyms": [ { "synonym": "P4HA" } ] }, "assessed_biomarker_entity_id": "NCBI: 5033", "assessed_entity_type": "gene", "specimen": [ { "name": "skin epidermis", "id": "UBERON:0001003", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0001003", "loinc_code": "" } ], "evidence_source": [ { "id": "32053263", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32053263", "evidence_list": [ { "evidence": "We studied further the significance of one of the genes, prolyl 4-hydroxylase subunit alpha 1 (P4HA1), in melanoma progression. P4HA1 depletion in melanoma cells reduced cell adhesion, invasion, and viability in vitro. Taken together, P4HA1 is an interesting potential prognostic marker and therapeutic target in primary melanomas, influencing many aspects of melanoma tumor progression." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0001003" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_4159" }, "synonyms": [ { "id": "DOID:4159", "name": "CA - skin cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_4159" }, { "id": "DOID:4159", "name": "malignant neoplasm of skin", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_4159" }, { "id": "DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_4159" } ] }, "evidence_source": [ { "id": "32053263", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32053263", "evidence_list": [ { "evidence": "We studied further the significance of one of the genes, prolyl 4-hydroxylase subunit alpha 1 (P4HA1), in melanoma progression. P4HA1 depletion in melanoma cells reduced cell adhesion, invasion, and viability in vitro. Taken together, P4HA1 is an interesting potential prognostic marker and therapeutic target in primary melanomas, influencing many aspects of melanoma tumor progression." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Prolyl 4-hydroxylase subunit alpha 1 (P4HA1) is a biomarker of poor prognosis in primary melanomas, and its depletion inhibits melanoma cell invasion and disrupts tumor blood vessel walls.", "journal": "Molecular oncology", "authors": "Eriksson J, Le Joncour V, Jahkola T, Juteau S, Laakkonen P, Saksela O, Hölttä E", "date": "2020-02-14", "evidence": [], "reference": [ { "id": "32053263", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32053263" } ] } ], "biomarker_canonical_id": "AN6502", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "f": "frequency", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6503-1", "biomarker_component": [ { "biomarker": "increased GDF15 level", "assessed_biomarker_entity": { "recommended_name": "Macrophage inhibitory cytokine 1", "synonyms": [ { "synonym": "GDF-15" }, { "synonym": "Macrophage inhibitory cytokine 1" }, { "synonym": "MIC-1" }, { "synonym": "NSAID-activated gene 1 protein" }, { "synonym": "NAG-1" }, { "synonym": "NSAID-regulated gene 1 protein" }, { "synonym": "NRG-1" }, { "synonym": "Placental TGF-beta" }, { "synonym": "Placental bone morphogenetic protein" }, { "synonym": "Prostate differentiation factor" } ] }, "assessed_biomarker_entity_id": "UPKB:Q99988", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "16428484", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/16428484", "evidence_list": [ { "evidence": "Ninety percent of patients with pancreatic cancer had MIC-1 levels >2 SD above age-matched controls. By logistic regression analysis, MIC-1 and CA19-9 were significant independent predictors of diagnosis. Receiver operating characteristic curve analysis showed that MIC-1 was significantly better than CA19-9 in differentiating patients with pancreatic cancer from healthy controls (area under the curve is 0.99 and 0.78, respectively; P = 0.003), but not in distinguishing pancreatic cancer from chronic pancreatitis (area under the curve of 0.81 and 0.74, respectively; P = 0.63). In the differentiation of patients with resectable pancreatic cancer from controls, serum MIC-1 outperforms other markers including CA19-9." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:1793", "recommended_name": { "id": "DOID:1793", "name": "pancreatic cancer", "description": "An endocrine gland cancer located_in the pancreas.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, "synonyms": [ { "id": "DOID:1793", "name": "Ca head of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "Ca body of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "pancreatic tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "malignant neoplasm of tail of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "malignant neoplasm of head of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "pancreatic neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "Ca tail of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "pancreas neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "malignant neoplasm of body of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" } ] }, "evidence_source": [ { "id": "16428484", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/16428484", "evidence_list": [ { "evidence": "Ninety percent of patients with pancreatic cancer had MIC-1 levels >2 SD above age-matched controls. By logistic regression analysis, MIC-1 and CA19-9 were significant independent predictors of diagnosis. Receiver operating characteristic curve analysis showed that MIC-1 was significantly better than CA19-9 in differentiating patients with pancreatic cancer from healthy controls (area under the curve is 0.99 and 0.78, respectively; P = 0.003), but not in distinguishing pancreatic cancer from chronic pancreatitis (area under the curve of 0.81 and 0.74, respectively; P = 0.63). In the differentiation of patients with resectable pancreatic cancer from controls, serum MIC-1 outperforms other markers including CA19-9." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Serum markers in patients with resectable pancreatic adenocarcinoma: macrophage inhibitory cytokine 1 versus CA19-9.", "journal": "Clinical cancer research : an official journal of the American Association for Cancer Research", "authors": "Koopmann J, Rosenzweig CN, Zhang Z, Canto MI, Brown DA, Hunter M, Yeo C, Chan DW, Breit SN, Goggins M", "date": "2006-01-24", "evidence": [], "reference": [ { "id": "16428484", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/16428484" } ] } ], "biomarker_canonical_id": "AN6503", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6504-1", "biomarker_component": [ { "biomarker": "increased BNIP3L level", "assessed_biomarker_entity": { "recommended_name": "BCL2/Adenovirus E1B 19 kDa protein-interacting protein 3-like", "synonyms": [ { "synonym": "Adenovirus E1B19K-binding protein B5" }, { "synonym": "BCL2/adenovirus E1B 19 kDa protein-interacting protein 3A" }, { "synonym": "NIP3-like protein X" }, { "synonym": "NIP3L" } ] }, "assessed_biomarker_entity_id": "UPKB:O60238", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "32620611", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32620611", "evidence_list": [ { "evidence": "A specific antibody response was raised against an antigen identified as BNIP3L, which correlated with a good prognosis. Medium and high expression of BNIP3L was also linked with longer overall survival. BNIP3L is a candidate prognostic marker of clinical outcome of melanoma patients treated with AGI-101H, and may be considered as a prediction marker for patient survival." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_4159" }, "synonyms": [ { "id": "DOID:4159", "name": "CA - skin cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_4159" }, { "id": "DOID:4159", "name": "malignant neoplasm of skin", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_4159" }, { "id": "DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_4159" } ] }, "evidence_source": [ { "id": "32620611", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32620611", "evidence_list": [ { "evidence": "A specific antibody response was raised against an antigen identified as BNIP3L, which correlated with a good prognosis. Medium and high expression of BNIP3L was also linked with longer overall survival. BNIP3L is a candidate prognostic marker of clinical outcome of melanoma patients treated with AGI-101H, and may be considered as a prediction marker for patient survival." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "BNIP3L Is a New Autophagy Related Prognostic Biomarker for Melanoma Patients Treated With AGI-101H.", "journal": "Anticancer research", "authors": "Kazimierczak U, Kolenda T, Kowalczyk D, Mackiewicz J, Mackiewicz A", "date": "2020-07-06", "evidence": [], "reference": [ { "id": "32620611", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32620611" } ] } ], "biomarker_canonical_id": "AN6504", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "w": "weight", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6505-1", "biomarker_component": [ { "biomarker": "increased GPC6 level", "assessed_biomarker_entity": { "recommended_name": "Glypican 6", "synonyms": [ { "synonym": "OMIMD1" } ] }, "assessed_biomarker_entity_id": "NCBI: 10082", "assessed_entity_type": "gene", "specimen": [ { "name": "skin epidermis", "id": "UBERON:0001003", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0001003", "loinc_code": "" } ], "evidence_source": [ { "id": "31199813", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31199813", "evidence_list": [ { "evidence": "GPC6 expression was up-regulated in a melanoma cell line compared to normal melanocytes and in metastatic melanoma compared to primary melanoma. Together, our findings identified GPC6 as an early biomarker for melanoma metastatic progression, one that can be regulated by miR-509-3p." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0001003" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_4159" }, "synonyms": [ { "id": "DOID:4159", "name": "CA - skin cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_4159" }, { "id": "DOID:4159", "name": "malignant neoplasm of skin", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_4159" }, { "id": "DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_4159" } ] }, "evidence_source": [ { "id": "31199813", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31199813", "evidence_list": [ { "evidence": "GPC6 expression was up-regulated in a melanoma cell line compared to normal melanocytes and in metastatic melanoma compared to primary melanoma. Together, our findings identified GPC6 as an early biomarker for melanoma metastatic progression, one that can be regulated by miR-509-3p." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Glypican 6 is a putative biomarker for metastatic progression of cutaneous melanoma.", "journal": "PloS one", "authors": "Li Y, Li M, Shats I, Krahn JM, Flake GP, Umbach DM, Li X, Li L", "date": "2019-06-15", "evidence": [], "reference": [ { "id": "31199813", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31199813" } ] } ], "biomarker_canonical_id": "AN6505", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "f": "frequency", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6506-1", "biomarker_component": [ { "biomarker": "decreased MIR-125A-5P level", "assessed_biomarker_entity": { "recommended_name": "miRNA-125a-5p", "synonyms": [] }, "assessed_biomarker_entity_id": "MRB:MIMAT0000443", "assessed_entity_type": "RNA", "specimen": [ { "name": "skin epidermis", "id": "UBERON:0001003", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0001003", "loinc_code": "" } ], "evidence_source": [ { "id": "31325708", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31325708", "evidence_list": [ { "evidence": "miR-125a-5p downregulation was associated with recurrent disease in a panel of high-risk HNSCC and then confirmed poor survival associated with low expression in HNSCC via the Cancer Genome Atlas, suggesting that miR-125a-5p acts as a tumor suppressor miRNA. results reveal that in patients who developed a local recurrence, there was an associated decreased in miR-125a-5p expression, compared to patients who did not have evidence of disease (P = .0036), out of a total of 77 evaluable patient samples analyzed. patients with low levels of miR-125a-5p is associated with a worse overall survival than patients with high levels of miR-125a-5p (P = .006)." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0001003" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:11934", "recommended_name": { "id": "DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11934" }, "synonyms": [ { "id": "DOID:11934", "name": "head and neck neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11934" }, { "id": "DOID:11934", "name": "head/neck neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11934" }, { "id": "DOID:11934", "name": "head and neck tumours", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11934" }, { "id": "DOID:11934", "name": "tumor of head and neck", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11934" } ] }, "evidence_source": [ { "id": "31325708", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31325708", "evidence_list": [ { "evidence": "miR-125a-5p downregulation was associated with recurrent disease in a panel of high-risk HNSCC and then confirmed poor survival associated with low expression in HNSCC via the Cancer Genome Atlas, suggesting that miR-125a-5p acts as a tumor suppressor miRNA. results reveal that in patients who developed a local recurrence, there was an associated decreased in miR-125a-5p expression, compared to patients who did not have evidence of disease (P = .0036), out of a total of 77 evaluable patient samples analyzed. patients with low levels of miR-125a-5p is associated with a worse overall survival than patients with high levels of miR-125a-5p (P = .006)." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "miR-125a-5p Functions as Tumor Suppressor microRNA And Is a Marker of Locoregional Recurrence And Poor prognosis in Head And Neck Cancer.", "journal": "Neoplasia (New York, N.Y.)", "authors": "Vo DT, Karanam NK, Ding L, Saha D, Yordy JS, Giri U, Heymach JV, Story MD", "date": "2019-07-22", "evidence": [], "reference": [ { "id": "31325708", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31325708" } ] } ], "biomarker_canonical_id": "AN6506", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "f": "frequency", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6507-1", "biomarker_component": [ { "biomarker": "increased GLT8D1 level", "assessed_biomarker_entity": { "recommended_name": "Glycosyltransferase 8 domain containing 1", "synonyms": [ { "synonym": "AD-017" }, { "synonym": "MSTP139" } ] }, "assessed_biomarker_entity_id": "NCBI: 55830", "assessed_entity_type": "gene", "specimen": [ { "name": "skin epidermis", "id": "UBERON:0001003", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0001003", "loinc_code": "" } ], "evidence_source": [ { "id": "31305325", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31305325", "evidence_list": [ { "evidence": "The GEO data analysis exhibited that the GLT8D1 mRNA expression was upregulated in the melanoma samples compared with the benign nevus samples. Furthermore, the GLT8D1 protein expression in cutaneous melanoma was higher than that in mucosal melanoma (P = 0.001). The high GLT8D1 protein expression was remarkably correlated with Clark level (P = 0.027), AJCC stage (P = 0.003), ulceration status (P = 0.041) Ki-67 expression (P = 0.030) and especially with histopathological type (P = 0.001). The results of the Kaplan‚ÄìMeier survival and Cox regression analyses revealed that cutaneous melanoma patients with high GLT8D1 expression (P = 0.036), Clark level (P = 0.018) and advanced AJCC stage (P = 0.003) encountered poor overall survival. Overall survival (P = 0.040) and progression free survival (P = 0.019) were worse for the patients with high GLT8D1 expression than for the patients with low expression. These data implied that GLT8D1 could be an independent prognostic factor for an unfavorable prognosis in cutaneous malignant melanoma patients and that GLT8D1 overexpression might serve as a novel prognostic biomarker." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0001003" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_4159" }, "synonyms": [ { "id": "DOID:4159", "name": "CA - skin cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_4159" }, { "id": "DOID:4159", "name": "malignant neoplasm of skin", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_4159" }, { "id": "DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_4159" } ] }, "evidence_source": [ { "id": "31305325", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31305325", "evidence_list": [ { "evidence": "The GEO data analysis exhibited that the GLT8D1 mRNA expression was upregulated in the melanoma samples compared with the benign nevus samples. Furthermore, the GLT8D1 protein expression in cutaneous melanoma was higher than that in mucosal melanoma (P = 0.001). The high GLT8D1 protein expression was remarkably correlated with Clark level (P = 0.027), AJCC stage (P = 0.003), ulceration status (P = 0.041) Ki-67 expression (P = 0.030) and especially with histopathological type (P = 0.001). The results of the Kaplan‚ÄìMeier survival and Cox regression analyses revealed that cutaneous melanoma patients with high GLT8D1 expression (P = 0.036), Clark level (P = 0.018) and advanced AJCC stage (P = 0.003) encountered poor overall survival. Overall survival (P = 0.040) and progression free survival (P = 0.019) were worse for the patients with high GLT8D1 expression than for the patients with low expression. These data implied that GLT8D1 could be an independent prognostic factor for an unfavorable prognosis in cutaneous malignant melanoma patients and that GLT8D1 overexpression might serve as a novel prognostic biomarker." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "GLT8D1 overexpression as a novel prognostic biomarker in human cutaneous melanoma.", "journal": "Melanoma research", "authors": "Hu H, Li Z, Zhou Y, Zhang Y, Zhao L, Zhao W, Huang Y, Song X", "date": "2019-07-16", "evidence": [], "reference": [ { "id": "31305325", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31305325" } ] } ], "biomarker_canonical_id": "AN6507", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "f": "frequency", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6508-1", "biomarker_component": [ { "biomarker": "decreased MIR-1231 level", "assessed_biomarker_entity": { "recommended_name": "miRNA-1231", "synonyms": [] }, "assessed_biomarker_entity_id": "MRB:MI0006321", "assessed_entity_type": "RNA", "specimen": [ { "name": "prostate gland", "id": "UBERON:0002367", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0002367", "loinc_code": "" } ], "evidence_source": [ { "id": "31822000", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31822000", "evidence_list": [ { "evidence": "miR-1231 expression was downregulated in both prostate cancer tissues and cell lines. Downregulation of miR-1231 was significantly associated with lymph node metastasis, higher TNM stage, higher clinical stage, and shorter overall survival. The expression of miR-1231 was predicted as a prognostic factor for prostate cancer patients." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0002367" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, "synonyms": [ { "id": "DOID:10283", "name": "prostate neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "NGP - new growth of prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "tumor of the prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostate cancer, familial", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostatic neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "malignant tumor of the prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "hereditary prostate cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostatic cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" } ] }, "evidence_source": [ { "id": "31822000", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31822000", "evidence_list": [ { "evidence": "miR-1231 expression was downregulated in both prostate cancer tissues and cell lines. Downregulation of miR-1231 was significantly associated with lymph node metastasis, higher TNM stage, higher clinical stage, and shorter overall survival. The expression of miR-1231 was predicted as a prognostic factor for prostate cancer patients." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "miR-1231 Is Downregulated in Prostate Cancer with Prognostic and Functional Implications.", "journal": "Oncology research and treatment", "authors": "Wang Y, Zhang Q, Guo B, Feng J, Zhao D", "date": "2019-12-11", "evidence": [], "reference": [ { "id": "31822000", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31822000" } ] } ], "biomarker_canonical_id": "AN6508", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "c": "condition", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6509-1", "biomarker_component": [ { "biomarker": "increased YAP1 level", "assessed_biomarker_entity": { "recommended_name": "Yes-associated protein 1", "synonyms": [ { "synonym": "Yes-associated protein 1" }, { "synonym": "Protein yorkie homolog" }, { "synonym": "Yes-associated protein YAP65 homolog" } ] }, "assessed_biomarker_entity_id": "UPKB:P46937", "assessed_entity_type": "protein", "specimen": [ { "name": "pancreas", "id": "UBERON:0001264", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0001264", "loinc_code": "" } ], "evidence_source": [ { "id": "32054505", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32054505", "evidence_list": [ { "evidence": "Mass spectrometry based proteomics showed that YAP1 is the top upregulated protein in pancreatic cancer tissue when compared to normal controls (log2 fold change 6.4; p = 5E-06). Prognostic analysis of YAP1 demonstrated a significant correlation between mRNA expression level data and reduced overall survival (p = 0.001). In addition, TMA and immunohistochemistry analysis suggested that YAP1 protein expression is an independent predictor of poor overall survival [hazard ratio (HR) 1.870, 95% confidence interval (CI) 1.224‚Äì2.855, p = 0.004], as well as reduced disease-free survival (HR 1.950, 95% CI 1.299‚Äì2.927, p = 0.001). Bioinformatic analyses coupled with in vitro assays indicated that YAP1 is involved in the transcriptional control of target genes, associated with extracellular matrix remodeling, which could be modified by selected substances disrupting the YAP1-TEAD interaction. We demonstrate that YAP1 is an independent prognostic marker associated with recurrence and unfavorable survival in pancreatic cancer. We also show that inhibition of YAP1/TEAD interaction interferes with the expression of AREG, CTGF, CYR61, and MSLN suggesting that YAP1 transcriptional activity may affect the development and persistence of a fibrotic tumor microenvironment. YAP1 is thus considered as a clinically and biologically relevant biomarker derived from pancreatic cancer tissue." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0001264" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:1793", "recommended_name": { "id": "DOID:1793", "name": "pancreatic cancer", "description": "An endocrine gland cancer located_in the pancreas.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, "synonyms": [ { "id": "DOID:1793", "name": "Ca head of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "Ca body of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "pancreatic tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "malignant neoplasm of tail of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "malignant neoplasm of head of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "pancreatic neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "Ca tail of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "pancreas neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "malignant neoplasm of body of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" } ] }, "evidence_source": [ { "id": "32054505", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32054505", "evidence_list": [ { "evidence": "Mass spectrometry based proteomics showed that YAP1 is the top upregulated protein in pancreatic cancer tissue when compared to normal controls (log2 fold change 6.4; p = 5E-06). Prognostic analysis of YAP1 demonstrated a significant correlation between mRNA expression level data and reduced overall survival (p = 0.001). In addition, TMA and immunohistochemistry analysis suggested that YAP1 protein expression is an independent predictor of poor overall survival [hazard ratio (HR) 1.870, 95% confidence interval (CI) 1.224‚Äì2.855, p = 0.004], as well as reduced disease-free survival (HR 1.950, 95% CI 1.299‚Äì2.927, p = 0.001). Bioinformatic analyses coupled with in vitro assays indicated that YAP1 is involved in the transcriptional control of target genes, associated with extracellular matrix remodeling, which could be modified by selected substances disrupting the YAP1-TEAD interaction. We demonstrate that YAP1 is an independent prognostic marker associated with recurrence and unfavorable survival in pancreatic cancer. We also show that inhibition of YAP1/TEAD interaction interferes with the expression of AREG, CTGF, CYR61, and MSLN suggesting that YAP1 transcriptional activity may affect the development and persistence of a fibrotic tumor microenvironment. YAP1 is thus considered as a clinically and biologically relevant biomarker derived from pancreatic cancer tissue." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "YAP1 is an independent prognostic marker in pancreatic cancer and associated with extracellular matrix remodeling.", "journal": "Journal of translational medicine", "authors": "Zhou Q, Bauden M, Andersson R, Hu D, Marko-Varga G, Xu J, Sasor A, Dai H, Pawłowski K, Said Hilmersson K, Chen X, Ansari D", "date": "2020-02-15", "evidence": [], "reference": [ { "id": "32054505", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32054505" } ] } ], "biomarker_canonical_id": "AN6509", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6510-1", "biomarker_component": [ { "biomarker": "increased ASPM level", "assessed_biomarker_entity": { "recommended_name": "Abnormal spindle-like microcephaly-associated protein", "synonyms": [ { "synonym": "ASP" }, { "synonym": "Calmbp1" }, { "synonym": "MCPH5" } ] }, "assessed_biomarker_entity_id": "NCBI: 259266", "assessed_entity_type": "gene", "specimen": [ { "name": "urinary bladder", "id": "UBERON:0001255", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0001255", "loinc_code": "" } ], "evidence_source": [ { "id": "32274607", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32274607", "evidence_list": [ { "evidence": "The upregulation of ASPM expression and the downregulation of TEF expression were observed in bladder cancer tissues compared to adjacent normal tissues, and these levels were correlated with high-grade tumors, advanced stage disease and the presence of metastasis. Both genes had the ability to predict metastatic association with sensitivity (84.62%) and specificity (68.42%; *P < 0.001) for the ASPM gene and for the TEF gene with sensitivity (80.77%) and specificity (78.95%; *P < 0.001). Additionally, Kaplan‚ÄìMeier survival analysis indicated that elevated ASPM expression levels and reduced TEF expression levels significantly correlated with decreased overall survival and progression-free survival. The current analysis concludes that ASPM and TEF expressions might be used as potential biomarkers in bladder cancer patients." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0001255" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11054" }, "synonyms": [ { "id": "DOID:11054", "name": "tumor of the bladder", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11054" }, { "id": "DOID:11054", "name": "bladder cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11054" } ] }, "evidence_source": [ { "id": "32274607", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32274607", "evidence_list": [ { "evidence": "The upregulation of ASPM expression and the downregulation of TEF expression were observed in bladder cancer tissues compared to adjacent normal tissues, and these levels were correlated with high-grade tumors, advanced stage disease and the presence of metastasis. Both genes had the ability to predict metastatic association with sensitivity (84.62%) and specificity (68.42%; *P < 0.001) for the ASPM gene and for the TEF gene with sensitivity (80.77%) and specificity (78.95%; *P < 0.001). Additionally, Kaplan‚ÄìMeier survival analysis indicated that elevated ASPM expression levels and reduced TEF expression levels significantly correlated with decreased overall survival and progression-free survival. The current analysis concludes that ASPM and TEF expressions might be used as potential biomarkers in bladder cancer patients." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Evaluation of ASPM and TEF Gene Expressions as Potential Biomarkers for Bladder Cancer.", "journal": "Biochemical genetics", "authors": "Saleh AA, Gohar SF, Hemida AS, Elgharbawy M, Soliman SE", "date": "2020-04-11", "evidence": [], "reference": [ { "id": "32274607", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32274607" } ] } ], "biomarker_canonical_id": "AN6510", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "w": "weight", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6511-1", "biomarker_component": [ { "biomarker": "decreased TEF level", "assessed_biomarker_entity": { "recommended_name": "Thyrotroph embryonic factor", "synonyms": [] }, "assessed_biomarker_entity_id": "NCBI: 7008", "assessed_entity_type": "gene", "specimen": [ { "name": "urinary bladder", "id": "UBERON:0001255", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0001255", "loinc_code": "" } ], "evidence_source": [ { "id": "32274607", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32274607", "evidence_list": [ { "evidence": "The upregulation of ASPM expression and the downregulation of TEF expression were observed in bladder cancer tissues compared to adjacent normal tissues, and these levels were correlated with high-grade tumors, advanced stage disease and the presence of metastasis. Both genes had the ability to predict metastatic association with sensitivity (84.62%) and specificity (68.42%; *P < 0.001) for the ASPM gene and for the TEF gene with sensitivity (80.77%) and specificity (78.95%; *P < 0.001). Additionally, Kaplan‚ÄìMeier survival analysis indicated that elevated ASPM expression levels and reduced TEF expression levels significantly correlated with decreased overall survival and progression-free survival. The current analysis concludes that ASPM and TEF expressions might be used as potential biomarkers in bladder cancer patients." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0001255" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11054" }, "synonyms": [ { "id": "DOID:11054", "name": "tumor of the bladder", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11054" }, { "id": "DOID:11054", "name": "bladder cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11054" } ] }, "evidence_source": [ { "id": "32274607", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32274607", "evidence_list": [ { "evidence": "The upregulation of ASPM expression and the downregulation of TEF expression were observed in bladder cancer tissues compared to adjacent normal tissues, and these levels were correlated with high-grade tumors, advanced stage disease and the presence of metastasis. Both genes had the ability to predict metastatic association with sensitivity (84.62%) and specificity (68.42%; *P < 0.001) for the ASPM gene and for the TEF gene with sensitivity (80.77%) and specificity (78.95%; *P < 0.001). Additionally, Kaplan‚ÄìMeier survival analysis indicated that elevated ASPM expression levels and reduced TEF expression levels significantly correlated with decreased overall survival and progression-free survival. The current analysis concludes that ASPM and TEF expressions might be used as potential biomarkers in bladder cancer patients." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Evaluation of ASPM and TEF Gene Expressions as Potential Biomarkers for Bladder Cancer.", "journal": "Biochemical genetics", "authors": "Saleh AA, Gohar SF, Hemida AS, Elgharbawy M, Soliman SE", "date": "2020-04-11", "evidence": [], "reference": [ { "id": "32274607", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32274607" } ] } ], "biomarker_canonical_id": "AN6511", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "c": "condition", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6512-1", "biomarker_component": [ { "biomarker": "increased A1AT level", "assessed_biomarker_entity": { "recommended_name": "Alpha-1-antitrypsin", "synonyms": [ { "synonym": "Alpha-1 protease inhibitor" }, { "synonym": "Alpha-1-antiproteinase" }, { "synonym": "Serpin A1" } ] }, "assessed_biomarker_entity_id": "UPKB:P01009", "assessed_entity_type": "protein", "specimen": [ { "name": "urine", "id": "UBERON:0001088", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0001088", "loinc_code": "" } ], "evidence_source": [ { "id": "21459797", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/21459797", "evidence_list": [ { "evidence": "Increased levels of urinary A1AT glycoprotein were indicative of the presence of bladder cancer (P < 0.0001) and augmented voided urine cytology results. Application of glycoprotein enrichment provided novel candidates for further investigation as biomarkers for the noninvasive detection of bladder cancer." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0001088" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11054" }, "synonyms": [ { "id": "DOID:11054", "name": "tumor of the bladder", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11054" }, { "id": "DOID:11054", "name": "bladder cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11054" } ] }, "evidence_source": [ { "id": "21459797", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/21459797", "evidence_list": [ { "evidence": "Increased levels of urinary A1AT glycoprotein were indicative of the presence of bladder cancer (P < 0.0001) and augmented voided urine cytology results. Application of glycoprotein enrichment provided novel candidates for further investigation as biomarkers for the noninvasive detection of bladder cancer." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Urinary glycoprotein biomarker discovery for bladder cancer detection using LC/MS-MS and label-free quantification.", "journal": "Clinical cancer research : an official journal of the American Association for Cancer Research", "authors": "Yang N, Feng S, Shedden K, Xie X, Liu Y, Rosser CJ, Lubman DM, Goodison S", "date": "2011-04-05", "evidence": [], "reference": [ { "id": "21459797", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/21459797" } ] } ], "biomarker_canonical_id": "AN6512", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "c": "condition", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6513-1", "biomarker_component": [ { "biomarker": "increased OPN level", "assessed_biomarker_entity": { "recommended_name": "Osteopontin", "synonyms": [ { "synonym": "Bone sialoprotein 1" }, { "synonym": "Nephropontin" }, { "synonym": "Secreted phosphoprotein 1" }, { "synonym": "SPP-1" }, { "synonym": "Urinary stone protein" }, { "synonym": "Uropontin" } ] }, "assessed_biomarker_entity_id": "UPKB:P10451", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "15006928", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/15006928", "evidence_list": [ { "evidence": "Serum OPN levels, as measured by ELISA, were elevated in the sera of 50 patients with resectable pancreatic adenocarcinoma compared to 22 healthy control individuals (mean +/- SD for OPN was 482 +/- 170 ng/ml and 204 +/- 65 ng/ml, respectively; P < 0.001). Serum OPN may have utility as a diagnostic marker in patients with pancreatic cancer." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:1793", "recommended_name": { "id": "DOID:1793", "name": "pancreatic cancer", "description": "An endocrine gland cancer located_in the pancreas.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, "synonyms": [ { "id": "DOID:1793", "name": "Ca head of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "Ca body of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "pancreatic tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "malignant neoplasm of tail of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "malignant neoplasm of head of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "pancreatic neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "Ca tail of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "pancreas neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "malignant neoplasm of body of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" } ] }, "evidence_source": [ { "id": "15006928", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/15006928", "evidence_list": [ { "evidence": "Serum OPN levels, as measured by ELISA, were elevated in the sera of 50 patients with resectable pancreatic adenocarcinoma compared to 22 healthy control individuals (mean +/- SD for OPN was 482 +/- 170 ng/ml and 204 +/- 65 ng/ml, respectively; P < 0.001). Serum OPN may have utility as a diagnostic marker in patients with pancreatic cancer." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Evaluation of osteopontin as biomarker for pancreatic adenocarcinoma.", "journal": "Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology", "authors": "Koopmann J, Fedarko NS, Jain A, Maitra A, Iacobuzio-Donahue C, Rahman A, Hruban RH, Yeo CJ, Goggins M", "date": "2004-03-10", "evidence": [], "reference": [ { "id": "15006928", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/15006928" } ] } ], "biomarker_canonical_id": "AN6513", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6513-2", "biomarker_component": [ { "biomarker": "increased OPN level", "assessed_biomarker_entity": { "recommended_name": "Osteopontin", "synonyms": [ { "synonym": "Bone sialoprotein 1" }, { "synonym": "Nephropontin" }, { "synonym": "Secreted phosphoprotein 1" }, { "synonym": "SPP-1" }, { "synonym": "Urinary stone protein" }, { "synonym": "Uropontin" } ] }, "assessed_biomarker_entity_id": "UPKB:P10451", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "11926891", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/11926891", "evidence_list": [ { "evidence": "Osteopontin levels in plasma were significantly higher (P<.001) in 51 patients with epithelial ovarian cancer (486.5 ng/mL) compared with those of 107 healthy controls (147.1 ng/mL), 46 patients with benign ovarian disease (254.4 ng/mL), and 47 patients with other gynecologic cancers (260.9 ng/mL)." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:2394", "recommended_name": { "id": "DOID:2394", "name": "ovarian cancer", "description": "A female reproductive organ cancer that is located_in the ovary.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, "synonyms": [ { "id": "DOID:2394", "name": "primary ovarian cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "tumor of the Ovary", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "ovary neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "malignant tumour of ovary", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "malignant Ovarian tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "ovarian neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" } ] }, "evidence_source": [ { "id": "11926891", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/11926891", "evidence_list": [ { "evidence": "Osteopontin levels in plasma were significantly higher (P<.001) in 51 patients with epithelial ovarian cancer (486.5 ng/mL) compared with those of 107 healthy controls (147.1 ng/mL), 46 patients with benign ovarian disease (254.4 ng/mL), and 47 patients with other gynecologic cancers (260.9 ng/mL)." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Osteopontin as a potential diagnostic biomarker for ovarian cancer.", "journal": "JAMA", "authors": "Kim JH, Skates SJ, Uede T, Wong KK, Schorge JO, Feltmate CM, Berkowitz RS, Cramer DW, Mok SC", "date": "2002-04-03", "evidence": [], "reference": [ { "id": "11926891", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/11926891" } ] } ], "biomarker_canonical_id": "AN6513", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6514-1", "biomarker_component": [ { "biomarker": "increased TNFSF9 level", "assessed_biomarker_entity": { 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In addition, high TNFSF9 expression was significantly related to poor overall survival (OS) and relapse-free survival (RFS) in pancreatic cancer (OS HR = 2.02, P = 0.0012; RFS HR = 2.63, P = 0.022). These findings indicate that TNFSF9 can be serves as a prognostic biomarker in determining the prognosis of pancreatic cancer and is associated with different types of phenotypes of immune cell infiltration." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "TNFSF9 Is a Prognostic Biomarker and Correlated with Immune Infiltrates in Pancreatic Cancer.", "journal": "Journal of gastrointestinal cancer", "authors": "Wu J, Wang Y, Jiang Z", "date": "2020-02-23", "evidence": [], "reference": [ { "id": "32077004", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32077004" } ] } ], "biomarker_canonical_id": "AN6514", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6515-1", "biomarker_component": [ { "biomarker": "increased NCEH1 level", "assessed_biomarker_entity": { "recommended_name": "Neutral cholesterol ester hydrolase 1", "synonyms": [ { "synonym": "AADACL1" }, { "synonym": "NCEH" } ] }, "assessed_biomarker_entity_id": "NCBI: 57552", "assessed_entity_type": "gene", "specimen": [ { "name": "pancreas", "id": "UBERON:0001264", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0001264", "loinc_code": "" } ], "evidence_source": [ { "id": "33284889", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/33284889", "evidence_list": [ { "evidence": "Elevated ether lipid metabolism is one of the characteristics of cancer cells. 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Further, NCEH1 expression was higher in patients with regional lymph node involvement than in the control group." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0001264" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:1793", "recommended_name": { "id": "DOID:1793", "name": "pancreatic cancer", "description": "An endocrine gland cancer located_in the pancreas.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, "synonyms": [ { "id": "DOID:1793", "name": "Ca head of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "Ca body of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "pancreatic tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "malignant neoplasm of tail of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "malignant neoplasm of head of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "pancreatic neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "Ca tail of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "pancreas neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "malignant neoplasm of body of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" } ] }, "evidence_source": [ { "id": "33284889", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/33284889", "evidence_list": [ { "evidence": "Elevated ether lipid metabolism is one of the characteristics of cancer cells. 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Further, NCEH1 expression was higher in patients with regional lymph node involvement than in the control group." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "NCEH1 may be a prognostic biomarker for pancreatic cancer.", "journal": "International journal of clinical and experimental pathology", "authors": "Lu Y, Zhang L, Chen X, Zhang Q", "date": "2020-12-08", "evidence": [], "reference": [ { "id": "33284889", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/33284889" } ] } ], "biomarker_canonical_id": "AN6515", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6516-1", "biomarker_component": [ { "biomarker": "increased PSMD11 level", "assessed_biomarker_entity": { "recommended_name": "26S proteasome non-ATPase regulatory subunit 11", "synonyms": [ { "synonym": "26S proteasome regulatory subunit RPN6" }, { "synonym": "26S proteasome regulatory subunit S9" }, { "synonym": "26S proteasome regulatory subunit p44.5" } ] }, "assessed_biomarker_entity_id": "UPKB:O00231", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "32663515", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32663515", "evidence_list": [ { "evidence": "This exploratory study, using SWATH-MS analysis, identified potential prognostic biomarkers for PDAC in plasma (PTPRM and PTPRB) and plasma derived microparticles (PSMD11). 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Protein tyrosine phosphatases, PTPRM and PTPRB, were decreased in plasma of patients with poor PDAC prognosis, while proteasomal subunit PSMD11 was increased in microparticles of patients with poor prognosis." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "PSMD11, PTPRM and PTPRB as novel biomarkers of pancreatic cancer progression.", "journal": "Biochimica et biophysica acta. 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Protein tyrosine phosphatases, PTPRM and PTPRB, were decreased in plasma of patients with poor PDAC prognosis, while proteasomal subunit PSMD11 was increased in microparticles of patients with poor prognosis." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:1793", "recommended_name": { "id": "DOID:1793", "name": "pancreatic cancer", "description": "An endocrine gland cancer located_in the pancreas.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, "synonyms": [ { "id": "DOID:1793", "name": "Ca head of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "Ca body of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "pancreatic tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "malignant neoplasm of tail of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "malignant neoplasm of head of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "pancreatic neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "Ca tail of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "pancreas neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "malignant neoplasm of body of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" } ] }, "evidence_source": [ { "id": "32663515", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32663515", "evidence_list": [ { "evidence": "This exploratory study, using SWATH-MS analysis, identified potential prognostic biomarkers for PDAC in plasma (PTPRM and PTPRB) and plasma derived microparticles (PSMD11). Protein tyrosine phosphatases, PTPRM and PTPRB, were decreased in plasma of patients with poor PDAC prognosis, while proteasomal subunit PSMD11 was increased in microparticles of patients with poor prognosis." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "PSMD11, PTPRM and PTPRB as novel biomarkers of pancreatic cancer progression.", "journal": "Biochimica et biophysica acta. General subjects", "authors": "Sahni S, Krisp C, Molloy MP, Nahm C, Maloney S, Gillson J, Gill AJ, Samra J, Mittal A", "date": "2020-07-15", "evidence": [], "reference": [ { "id": "32663515", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32663515" } ] } ], "biomarker_canonical_id": "AN6518", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "f": "frequency", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6519-1", "biomarker_component": [ { "biomarker": "increased TYMS level", "assessed_biomarker_entity": { "recommended_name": "Thymidylate synthase", "synonyms": [ { "synonym": "DKCD" }, { "synonym": "HST422" }, { "synonym": "TMS" }, { "synonym": "TS" } ] }, "assessed_biomarker_entity_id": "NCBI: 7298", "assessed_entity_type": "gene", "specimen": [ { "name": "pancreas", "id": "UBERON:0001264", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0001264", "loinc_code": "" } ], "evidence_source": [ { "id": "31861032", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31861032", "evidence_list": [ { "evidence": "Upregulation of TYMS was associated with poor RFS in patients with pancreatic cancer (P = .021). Subgroup analysis revealed that TYMS upregulation was associated with poor RFS in clinical stage I/II (P = .0038). Higher TYMS expression was associated with worse OS (P = .014) (Fig. 3). Subgroup analysis further indicated that high TYMS expression significantly affected the OS of patients in histologic grades G1/G2 (P = .025) and clinical stages I/II (P = .023). patients with pancreatic cancer, higher TYMS expression is associated with advanced clinical stages and undesirable prognosis, and that TYMS could be used as a biomarker for diagnostic and prognostic evaluation in patients with pancreatic cancer." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0001264" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:1793", "recommended_name": { "id": "DOID:1793", "name": "pancreatic cancer", "description": "An endocrine gland cancer located_in the pancreas.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, "synonyms": [ { "id": "DOID:1793", "name": "Ca head of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "Ca body of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "pancreatic tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "malignant neoplasm of tail of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "malignant neoplasm of head of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "pancreatic neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "Ca tail of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "pancreas neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "malignant neoplasm of body of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" } ] }, "evidence_source": [ { "id": "31861032", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31861032", "evidence_list": [ { "evidence": "Upregulation of TYMS was associated with poor RFS in patients with pancreatic cancer (P = .021). Subgroup analysis revealed that TYMS upregulation was associated with poor RFS in clinical stage I/II (P = .0038). Higher TYMS expression was associated with worse OS (P = .014) (Fig. 3). Subgroup analysis further indicated that high TYMS expression significantly affected the OS of patients in histologic grades G1/G2 (P = .025) and clinical stages I/II (P = .023). patients with pancreatic cancer, higher TYMS expression is associated with advanced clinical stages and undesirable prognosis, and that TYMS could be used as a biomarker for diagnostic and prognostic evaluation in patients with pancreatic cancer." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "TYMS presents a novel biomarker for diagnosis and prognosis in patients with pancreatic cancer.", "journal": "Medicine", "authors": "Fu Z, Jiao Y, Li Y, Ji B, Jia B, Liu B", "date": "2019-12-22", "evidence": [], "reference": [ { "id": "31861032", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31861032" } ] } ], "biomarker_canonical_id": "AN6519", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6520-1", "biomarker_component": [ { "biomarker": "increased ST6GALNAC6 level", "assessed_biomarker_entity": { "recommended_name": "Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 6", "synonyms": [ { "synonym": "SIAT7-F" }, { "synonym": "SIAT7F" }, { "synonym": "ST6GALNACVI" } ] }, "assessed_biomarker_entity_id": "NCBI: 30815", "assessed_entity_type": "gene", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "30131287", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30131287", "evidence_list": [ { "evidence": "In patients with pancreatic cancer, 8.4% of subjects were Lewis (-), but only 41.9% of Lewis (-) subjects had CA19-9 values 37 U/mL) in 27.4% of Lewis (-) patients. CA19-9 can retain its utility as a biomarker in these patients in spite of Lewis (-) genotype. The area under the receiver operating characteristic (ROC) curve for CA19-9 as a diagnostic biomarker was 0.842 in Lewis (-) patients with pancreatic cancer." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:1793", "recommended_name": { "id": "DOID:1793", "name": "pancreatic cancer", "description": "An endocrine gland cancer located_in the pancreas.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, "synonyms": [ { "id": "DOID:1793", "name": "Ca head of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "Ca body of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "pancreatic tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "malignant neoplasm of tail of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "malignant neoplasm of head of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "pancreatic neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "Ca tail of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "pancreas neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "malignant neoplasm of body of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" } ] }, "evidence_source": [ { "id": "30131287", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30131287", "evidence_list": [ { "evidence": "In patients with pancreatic cancer, 8.4% of subjects were Lewis (-), but only 41.9% of Lewis (-) subjects had CA19-9 values 37 U/mL) in 27.4% of Lewis (-) patients. CA19-9 can retain its utility as a biomarker in these patients in spite of Lewis (-) genotype. The area under the receiver operating characteristic (ROC) curve for CA19-9 as a diagnostic biomarker was 0.842 in Lewis (-) patients with pancreatic cancer." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "New observations on the utility of CA19-9 as a biomarker in Lewis negative patients with pancreatic cancer.", "journal": "Pancreatology : official journal of the International Association of Pancreatology (IAP) ... [et al.]", "authors": "Luo G, Fan Z, Cheng H, Jin K, Guo M, Lu Y, Yang C, Fan K, Huang Q, Long J, Liu L, Xu J, Lu R, Ni Q, Warshaw AL, Liu C, Yu X", "date": "2018-08-23", "evidence": [], "reference": [ { "id": "30131287", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30131287" } ] } ], "biomarker_canonical_id": "AN6520", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "f": "frequency", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6521-1", "biomarker_component": [ { "biomarker": "Increased MMP2 level", "assessed_biomarker_entity": { "recommended_name": "Matrix metalloproteinase-2", "synonyms": [ { "synonym": "72 kDa gelatinase" }, { "synonym": "Gelatinase A" }, { "synonym": "Matrix metalloproteinase-2" }, { "synonym": "MMP-2" }, { "synonym": "TBE-1" } ] }, "assessed_biomarker_entity_id": "UPKB:P08253", "assessed_entity_type": "protein", "specimen": [ { "name": "breast", "id": "UBERON:0000310", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000310", "loinc_code": "" } ], "evidence_source": [ { "id": "32176626", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32176626", "evidence_list": [ { "evidence": "We found ARHGDIB mediated epithelial-mesenchymal transition, and MMP2 is the key downstream effector of ARHGDIB." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000310" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "name": "breast cancer", "description": "A thoracic cancer that originates in the mammary gland.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, "synonyms": [ { "id": "DOID:1612", "name": "malignant tumor of the breast", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "breast tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "mammary cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "primary breast cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "mammary tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "malignant neoplasm of breast", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" } ] }, "evidence_source": [ { "id": "32176626", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32176626", "evidence_list": [ { "evidence": "We found ARHGDIB mediated epithelial-mesenchymal transition, and MMP2 is the key downstream effector of ARHGDIB." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Systematic investigation of biomarker-like role of ARHGDIB in breast cancer.", "journal": "Cancer biomarkers : section A of Disease markers", "authors": "Wang X, Bi X, Huang X, Wang B, Guo Q, Wu Z", "date": "2020-03-17", "evidence": [], "reference": [ { "id": "32176626", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32176626" } ] } ], "biomarker_canonical_id": "AN6521", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "c": "condition", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6522-1", "biomarker_component": [ { "biomarker": "increased ARHGDIB level", "assessed_biomarker_entity": { "recommended_name": "Rho GDP dissociation inhibitor protein", "synonyms": [ { "synonym": "Rho GDI 2" }, { "synonym": "Ly-GDI" }, { "synonym": "Rho-GDI beta" } ] }, "assessed_biomarker_entity_id": "UPKB:P52566", "assessed_entity_type": "protein", "specimen": [ { "name": "breast", "id": "UBERON:0000310", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000310", "loinc_code": "" } ], "evidence_source": [ { "id": "32176626", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32176626", "evidence_list": [ { "evidence": "We observed the expression of ARHGDIB is significantly higher in human breast cancer tissues compared with the benign tissues. ARHGDIB expression was positively correlated with tumor size, lymph node metastasis and TNM stage in breast cancer patients. Hence, our results suggested the significance and predictive role of ARHGDIB in breast cancer. High expression of ARHGDIB indicated the poor prognosis for breast cancer patients." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000310" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "name": "breast cancer", "description": "A thoracic cancer that originates in the mammary gland.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, "synonyms": [ { "id": "DOID:1612", "name": "malignant tumor of the breast", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "breast tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "mammary cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "primary breast cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "mammary tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "malignant neoplasm of breast", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" } ] }, "evidence_source": [ { "id": "32176626", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32176626", "evidence_list": [ { "evidence": "We observed the expression of ARHGDIB is significantly higher in human breast cancer tissues compared with the benign tissues. ARHGDIB expression was positively correlated with tumor size, lymph node metastasis and TNM stage in breast cancer patients. Hence, our results suggested the significance and predictive role of ARHGDIB in breast cancer. High expression of ARHGDIB indicated the poor prognosis for breast cancer patients." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Systematic investigation of biomarker-like role of ARHGDIB in breast cancer.", "journal": "Cancer biomarkers : section A of Disease markers", "authors": "Wang X, Bi X, Huang X, Wang B, Guo Q, Wu Z", "date": "2020-03-17", "evidence": [], "reference": [ { "id": "32176626", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32176626" } ] } ], "biomarker_canonical_id": "AN6522", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6523-1", "biomarker_component": [ { "biomarker": "decreased SMPD1 level", "assessed_biomarker_entity": { "recommended_name": "Acid sphingomyelinase", "synonyms": [ { "synonym": "Acid sphingomyelinase" }, { "synonym": "aSMase" } ] }, "assessed_biomarker_entity_id": "UPKB:P17405", "assessed_entity_type": "protein", "specimen": [ { "name": "ovary", "id": "UBERON:0000992", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000992", "loinc_code": "" } ], "evidence_source": [ { "id": "26125272", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/26125272", "evidence_list": [ { "evidence": "The levels of ASM were reducing with the development of ovarian cancer. ASM is higher expressed in normal cell than that in ovarian cancer, and can be a negative biomarker for the diagnosis of ovarian cancer. ASM can be developed a new drug for the ovarian cancer therapy." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000992" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:2394", "recommended_name": { "id": "DOID:2394", "name": "ovarian cancer", "description": "A female reproductive organ cancer that is located_in the ovary.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, "synonyms": [ { "id": "DOID:2394", "name": "primary ovarian cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "tumor of the Ovary", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "ovary neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "malignant tumour of ovary", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "malignant Ovarian tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "ovarian neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" } ] }, "evidence_source": [ { "id": "26125272", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/26125272", "evidence_list": [ { "evidence": "The levels of ASM were reducing with the development of ovarian cancer. ASM is higher expressed in normal cell than that in ovarian cancer, and can be a negative biomarker for the diagnosis of ovarian cancer. ASM can be developed a new drug for the ovarian cancer therapy." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Acid sphingomyelinase, a novel negative biomarker of ovarian cancer.", "journal": "European review for medical and pharmacological sciences", "authors": "Dai SY, Liu JJ, Sun XF, Wang N", "date": "2015-07-01", "evidence": [], "reference": [ { "id": "26125272", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/26125272" } ] } ], "biomarker_canonical_id": "AN6523", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "c": "condition", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6524-1", "biomarker_component": [ { "biomarker": "increased NFE2L2 level", "assessed_biomarker_entity": { "recommended_name": "Nuclear factor erythroid 2-related factor 2", "synonyms": [ { "synonym": "HEBP1" }, { "synonym": "IMDDHH" }, { "synonym": "NRF2" }, { "synonym": "Nrf-2" } ] }, "assessed_biomarker_entity_id": "NCBI: 4780", "assessed_entity_type": "gene", "specimen": [ { "name": "colon", "id": "UBERON:0001155", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0001155", "loinc_code": "" } ], "evidence_source": [ { "id": "32871287", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32871287", "evidence_list": [ { "evidence": "High NRF2 was associated with worse disease free survival (DFS) and/or overall survival (OS) in all datasets. NRF2 is shown to be a consistent, robust prognostic biomarker across all stages of colorectal cancer with additional clinical value to current known prognostic biomarkers." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0001155" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_9256" }, "synonyms": [] }, "evidence_source": [ { "id": "32871287", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32871287", "evidence_list": [ { "evidence": "High NRF2 was associated with worse disease free survival (DFS) and/or overall survival (OS) in all datasets. NRF2 is shown to be a consistent, robust prognostic biomarker across all stages of colorectal cancer with additional clinical value to current known prognostic biomarkers." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "NRF2 metagene signature is a novel prognostic biomarker in colorectal cancer.", "journal": "Cancer genetics", "authors": "O'Cathail SM, Wu CH, Lewis A, Holmes C, Hawkins MA, Maughan T", "date": "2020-09-02", "evidence": [], "reference": [ { "id": "32871287", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32871287" } ] } ], "biomarker_canonical_id": "AN6524", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6525-1", "biomarker_component": [ { "biomarker": "increased KRT15 level", "assessed_biomarker_entity": { "recommended_name": "Keratin-15", "synonyms": [ { "synonym": "CK15" }, { "synonym": "K15" }, { "synonym": "K1CO" } ] }, "assessed_biomarker_entity_id": "NCBI: 3866", "assessed_entity_type": "gene", "specimen": [ { "name": "colon", "id": "UBERON:0001155", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0001155", "loinc_code": "" } ], "evidence_source": [ { "id": "31884802", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31884802", "evidence_list": [ { "evidence": "QRT-PCR results revealed that the mRNA levels of KRT15 in colorectal cancer tissues were significantly higher compared with those in normal tissues (p<0.0001). The rates of KRT15 high-expression in colorectal cancer and normal tissues were 57.1% and 8.9%, respectively, and the difference was statistically significant (p<0.0001). KRT15 high-expression correlated with differentiation, T stage, lymph node metastasis and clinical stage in colorectal cancer (p<0.05). KRT15 overexpression predicted poor prognosis and could be used as an independent prognostic factor. These data indicate KRT15 is highly expressed in colorectal cancer and may serve as a prognostic biomarker." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0001155" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_9256" }, "synonyms": [] }, "evidence_source": [ { "id": "31884802", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31884802", "evidence_list": [ { "evidence": "QRT-PCR results revealed that the mRNA levels of KRT15 in colorectal cancer tissues were significantly higher compared with those in normal tissues (p<0.0001). The rates of KRT15 high-expression in colorectal cancer and normal tissues were 57.1% and 8.9%, respectively, and the difference was statistically significant (p<0.0001). KRT15 high-expression correlated with differentiation, T stage, lymph node metastasis and clinical stage in colorectal cancer (p<0.05). KRT15 overexpression predicted poor prognosis and could be used as an independent prognostic factor. These data indicate KRT15 is highly expressed in colorectal cancer and may serve as a prognostic biomarker." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "KRT15 overexpression predicts poor prognosis in colorectal cancer.", "journal": "Neoplasma", "authors": "Rao X, Wang J, Song HM, Deng B, Li JG", "date": "2019-12-31", "evidence": [], "reference": [ { "id": "31884802", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31884802" } ] } ], "biomarker_canonical_id": "AN6525", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "f": "frequency", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6526-1", "biomarker_component": [ { "biomarker": "increased MIR-135A-5P level", "assessed_biomarker_entity": { "recommended_name": "miRNA-135a-5p", "synonyms": [] }, "assessed_biomarker_entity_id": "MRB:MIMAT0000428", "assessed_entity_type": "RNA", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "27126269", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/27126269", "evidence_list": [ { "evidence": "Serum miR-135a-5p expression in colorectal cancer patients was higher than that in patients with colorectal polyps and healthy controls, suggesting that serum miR-135a-5p may prove to be an important biomarker for auxiliary diagnosis of colorectal cancer. The relative expression level of serum miR-135a-5p in colorectal cancer patients, colorectal polyps patients and healthy controls was 2.451 (1.107, 4.413), 0.946 (0.401, 1.942) and 0.949 (0.194, 1.415), respectively, indicating that it was significantly higher in colorectal cancer patients than that in the other two groups (U = 351.0, 313.0, both P < 0.001). Additionally, it was significantly correlated with different degrees of tumour differentiation (U = 215.0, P = 0.029) and different tumour stages (U = 202.0, P = 0.013)." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_9256" }, "synonyms": [] }, "evidence_source": [ { "id": "27126269", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/27126269", "evidence_list": [ { "evidence": "Serum miR-135a-5p expression in colorectal cancer patients was higher than that in patients with colorectal polyps and healthy controls, suggesting that serum miR-135a-5p may prove to be an important biomarker for auxiliary diagnosis of colorectal cancer. The relative expression level of serum miR-135a-5p in colorectal cancer patients, colorectal polyps patients and healthy controls was 2.451 (1.107, 4.413), 0.946 (0.401, 1.942) and 0.949 (0.194, 1.415), respectively, indicating that it was significantly higher in colorectal cancer patients than that in the other two groups (U = 351.0, 313.0, both P < 0.001). Additionally, it was significantly correlated with different degrees of tumour differentiation (U = 215.0, P = 0.029) and different tumour stages (U = 202.0, P = 0.013)." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Serum microRNA-135a-5p as an auxiliary diagnostic biomarker for colorectal cancer.", "journal": "Annals of clinical biochemistry", "authors": "Wang Q, Zhang H, Shen X, Ju S", "date": "2016-04-30", "evidence": [], "reference": [ { "id": "27126269", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/27126269" } ] } ], "biomarker_canonical_id": "AN6526", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "c": "condition", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6527-1", "biomarker_component": [ { "biomarker": "decreased B3GALT5-AS1 level", "assessed_biomarker_entity": { "recommended_name": "Putative uncharacterized protein B3GALT5-AS1", "synonyms": [ { "synonym": "B3GALT5 antisense RNA 1" }, { "synonym": "B3GALT5 antisense gene protein 1" } ] }, "assessed_biomarker_entity_id": "UPKB:P59052", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "32207329", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32207329", "evidence_list": [ { "evidence": "The level of B3GALT5-AS1 in CRC patients was significantly lower than that of healthy patients (p < 0.0001). B3GALT5-AS1 may be served as a diagnostic marker for distinguishing CRC patients from healthy people. Further exploration validated that high serum B3GALT5-AS1 level was related to tumor node metastasis (TNM) stage (p = 0.008) and histological differentiation (p = 0.027). Compared with the healthy control group, AUCROC of serum B3GALT5-AS1 in the CRC group was 0.762 with 95% CI: 0.698‚Äì0.826 (p < 0.0001)." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_9256" }, "synonyms": [] }, "evidence_source": [ { "id": "32207329", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32207329", "evidence_list": [ { "evidence": "The level of B3GALT5-AS1 in CRC patients was significantly lower than that of healthy patients (p < 0.0001). B3GALT5-AS1 may be served as a diagnostic marker for distinguishing CRC patients from healthy people. Further exploration validated that high serum B3GALT5-AS1 level was related to tumor node metastasis (TNM) stage (p = 0.008) and histological differentiation (p = 0.027). Compared with the healthy control group, AUCROC of serum B3GALT5-AS1 in the CRC group was 0.762 with 95% CI: 0.698‚Äì0.826 (p < 0.0001)." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Serum level of long noncoding RNA B3GALT5-AS1 as a diagnostic biomarker of colorectal cancer.", "journal": "Future oncology (London, England)", "authors": "Ding Y, Feng W, Ge JK, Dai L, Liu TT, Hua XY, Lu X, Ju SQ, Yu J", "date": "2020-03-25", "evidence": [], "reference": [ { "id": "32207329", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32207329" } ] } ], "biomarker_canonical_id": "AN6527", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "f": "frequency", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6528-1", "biomarker_component": [ { "biomarker": "increased MIR-10B level", "assessed_biomarker_entity": { "recommended_name": "miRNA-10b", "synonyms": [] }, "assessed_biomarker_entity_id": "MRB:MI0000267", "assessed_entity_type": "RNA", "specimen": [ { "name": "saliva", "id": "UBERON:0001836", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0001836", "loinc_code": "" } ], "evidence_source": [ { "id": "23560033", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/23560033", "evidence_list": [ { "evidence": "miR-10b*, miR-144, miR-21, and miR-451 in saliva supernatant were significantly upregulated in patients, with sensitivities of 89.7, 92.3, 84.6, 79.5, 43.6, 89.7, and 51.3% and specificities of 57.9, 47.4, 57.9%, 57.9, 89.5, 47.4, and 84.2%, respectively. We found distinctive miRNAs for esophageal cancer in both whole saliva and saliva supernatant. These miRNAs possess discriminatory power for detection of esophageal cancer. Because saliva collection is noninvasive and convenient, salivary miRNAs show great promise as biomarkers for detection of esophageal cancer in areas at high risk." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0001836" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, "synonyms": [ { "id": "DOID:5041", "name": "Ca lower third oesophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant tumor of abdominal esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "Ca middle third oesophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant neoplasm of upper third esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "esophagus cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" } ] }, "evidence_source": [ { "id": "23560033", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/23560033", "evidence_list": [ { "evidence": "miR-10b*, miR-144, miR-21, and miR-451 in saliva supernatant were significantly upregulated in patients, with sensitivities of 89.7, 92.3, 84.6, 79.5, 43.6, 89.7, and 51.3% and specificities of 57.9, 47.4, 57.9%, 57.9, 89.5, 47.4, and 84.2%, respectively. We found distinctive miRNAs for esophageal cancer in both whole saliva and saliva supernatant. These miRNAs possess discriminatory power for detection of esophageal cancer. Because saliva collection is noninvasive and convenient, salivary miRNAs show great promise as biomarkers for detection of esophageal cancer in areas at high risk." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Salivary microRNAs as promising biomarkers for detection of esophageal cancer.", "journal": "PloS one", "authors": "Xie Z, Chen G, Zhang X, Li D, Huang J, Yang C, Zhang P, Qin Y, Duan Y, Gong B, Li Z", "date": "2013-04-06", "evidence": [], "reference": [ { "id": "23560033", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/23560033" } ] } ], "biomarker_canonical_id": "AN6528", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "c": "condition", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6529-1", "biomarker_component": [ { "biomarker": "increased MIR-144 level", "assessed_biomarker_entity": { "recommended_name": "miRNA-144", "synonyms": [] }, "assessed_biomarker_entity_id": "MRB:MI0000460", "assessed_entity_type": "RNA", "specimen": [ { "name": "saliva", "id": "UBERON:0001836", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0001836", "loinc_code": "" } ], "evidence_source": [ { "id": "23560033", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/23560033", "evidence_list": [ { "evidence": "miR-10b*, miR-144, miR-21, and miR-451 in saliva supernatant were significantly upregulated in patients, with sensitivities of 89.7, 92.3, 84.6, 79.5, 43.6, 89.7, and 51.3% and specificities of 57.9, 47.4, 57.9%, 57.9, 89.5, 47.4, and 84.2%, respectively. We found distinctive miRNAs for esophageal cancer in both whole saliva and saliva supernatant. These miRNAs possess discriminatory power for detection of esophageal cancer. Because saliva collection is noninvasive and convenient, salivary miRNAs show great promise as biomarkers for detection of esophageal cancer in areas at high risk." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0001836" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, "synonyms": [ { "id": "DOID:5041", "name": "Ca lower third oesophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant tumor of abdominal esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "Ca middle third oesophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant neoplasm of upper third esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "esophagus cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" } ] }, "evidence_source": [ { "id": "23560033", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/23560033", "evidence_list": [ { "evidence": "miR-10b*, miR-144, miR-21, and miR-451 in saliva supernatant were significantly upregulated in patients, with sensitivities of 89.7, 92.3, 84.6, 79.5, 43.6, 89.7, and 51.3% and specificities of 57.9, 47.4, 57.9%, 57.9, 89.5, 47.4, and 84.2%, respectively. We found distinctive miRNAs for esophageal cancer in both whole saliva and saliva supernatant. These miRNAs possess discriminatory power for detection of esophageal cancer. Because saliva collection is noninvasive and convenient, salivary miRNAs show great promise as biomarkers for detection of esophageal cancer in areas at high risk." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Salivary microRNAs as promising biomarkers for detection of esophageal cancer.", "journal": "PloS one", "authors": "Xie Z, Chen G, Zhang X, Li D, Huang J, Yang C, Zhang P, Qin Y, Duan Y, Gong B, Li Z", "date": "2013-04-06", "evidence": [], "reference": [ { "id": "23560033", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/23560033" } ] } ], "biomarker_canonical_id": "AN6529", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "c": "condition", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6530-1", "biomarker_component": [ { "biomarker": "increased MIR-451 level", "assessed_biomarker_entity": { "recommended_name": "miRNA-451", "synonyms": [] }, "assessed_biomarker_entity_id": "MRB:MI0001729", "assessed_entity_type": "RNA", "specimen": [ { "name": "saliva", "id": "UBERON:0001836", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0001836", "loinc_code": "" } ], "evidence_source": [ { "id": "23560033", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/23560033", "evidence_list": [ { "evidence": "miR-10b*, miR-144, miR-21, and miR-451 in saliva supernatant were significantly upregulated in patients, with sensitivities of 89.7, 92.3, 84.6, 79.5, 43.6, 89.7, and 51.3% and specificities of 57.9, 47.4, 57.9%, 57.9, 89.5, 47.4, and 84.2%, respectively. We found distinctive miRNAs for esophageal cancer in both whole saliva and saliva supernatant. These miRNAs possess discriminatory power for detection of esophageal cancer. Because saliva collection is noninvasive and convenient, salivary miRNAs show great promise as biomarkers for detection of esophageal cancer in areas at high risk." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0001836" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, "synonyms": [ { "id": "DOID:5041", "name": "Ca lower third oesophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant tumor of abdominal esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "Ca middle third oesophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant neoplasm of upper third esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "esophagus cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" } ] }, "evidence_source": [ { "id": "23560033", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/23560033", "evidence_list": [ { "evidence": "miR-10b*, miR-144, miR-21, and miR-451 in saliva supernatant were significantly upregulated in patients, with sensitivities of 89.7, 92.3, 84.6, 79.5, 43.6, 89.7, and 51.3% and specificities of 57.9, 47.4, 57.9%, 57.9, 89.5, 47.4, and 84.2%, respectively. We found distinctive miRNAs for esophageal cancer in both whole saliva and saliva supernatant. These miRNAs possess discriminatory power for detection of esophageal cancer. Because saliva collection is noninvasive and convenient, salivary miRNAs show great promise as biomarkers for detection of esophageal cancer in areas at high risk." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Salivary microRNAs as promising biomarkers for detection of esophageal cancer.", "journal": "PloS one", "authors": "Xie Z, Chen G, Zhang X, Li D, Huang J, Yang C, Zhang P, Qin Y, Duan Y, Gong B, Li Z", "date": "2013-04-06", "evidence": [], "reference": [ { "id": "23560033", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/23560033" } ] } ], "biomarker_canonical_id": "AN6530", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6531-1", "biomarker_component": [ { "biomarker": "increased MIR-21 level", "assessed_biomarker_entity": { "recommended_name": "miRNA-21", "synonyms": [] }, "assessed_biomarker_entity_id": "MRB:MI0000077", "assessed_entity_type": "RNA", "specimen": [ { "name": "saliva", "id": "UBERON:0001836", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0001836", "loinc_code": "" } ], "evidence_source": [ { "id": "23560033", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/23560033", "evidence_list": [ { "evidence": "miR-10b*, miR-144, miR-21, and miR-451 in saliva supernatant were significantly upregulated in patients, with sensitivities of 89.7, 92.3, 84.6, 79.5, 43.6, 89.7, and 51.3% and specificities of 57.9, 47.4, 57.9%, 57.9, 89.5, 47.4, and 84.2%, respectively. We found distinctive miRNAs for esophageal cancer in both whole saliva and saliva supernatant. These miRNAs possess discriminatory power for detection of esophageal cancer. Because saliva collection is noninvasive and convenient, salivary miRNAs show great promise as biomarkers for detection of esophageal cancer in areas at high risk." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0001836" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, "synonyms": [ { "id": "DOID:5041", "name": "Ca lower third oesophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant tumor of abdominal esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "Ca middle third oesophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant neoplasm of upper third esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "esophagus cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" } ] }, "evidence_source": [ { "id": "23560033", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/23560033", "evidence_list": [ { "evidence": "miR-10b*, miR-144, miR-21, and miR-451 in saliva supernatant were significantly upregulated in patients, with sensitivities of 89.7, 92.3, 84.6, 79.5, 43.6, 89.7, and 51.3% and specificities of 57.9, 47.4, 57.9%, 57.9, 89.5, 47.4, and 84.2%, respectively. We found distinctive miRNAs for esophageal cancer in both whole saliva and saliva supernatant. These miRNAs possess discriminatory power for detection of esophageal cancer. Because saliva collection is noninvasive and convenient, salivary miRNAs show great promise as biomarkers for detection of esophageal cancer in areas at high risk." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Salivary microRNAs as promising biomarkers for detection of esophageal cancer.", "journal": "PloS one", "authors": "Xie Z, Chen G, Zhang X, Li D, Huang J, Yang C, Zhang P, Qin Y, Duan Y, Gong B, Li Z", "date": "2013-04-06", "evidence": [], "reference": [ { "id": "23560033", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/23560033" } ] } ], "biomarker_canonical_id": "AN6531", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "c": "condition", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6531-2", "biomarker_component": [ { "biomarker": "increased MIR-21 level", "assessed_biomarker_entity": { "recommended_name": "miRNA-21", "synonyms": [] }, "assessed_biomarker_entity_id": "MRB:MI0000077", "assessed_entity_type": "RNA", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "31030498", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31030498", "evidence_list": [ { "evidence": "Expression of circulating miR-21 was significantly elevated in breast cancer patients compared to healthy women (median miR-21 expression levels were 7.67¬±2.2 and 1.28¬±0.16, respectively; p<0.0001) Patients with upregulation of circulating miR-21 were associated with poor progression-free survival (median survival 72 vs 86 weeks, respectively; log-rank (Mantel-Cox) test, p=0.049). MiR-21 expression was upregulated in breast cancer patients and might serve as a therapeutic monitoring marker." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "name": "breast cancer", "description": "A thoracic cancer that originates in the mammary gland.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, "synonyms": [ { "id": "DOID:1612", "name": "malignant tumor of the breast", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "breast tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "mammary cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "primary breast cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "mammary tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "malignant neoplasm of breast", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" } ] }, "evidence_source": [ { "id": "31030498", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31030498", "evidence_list": [ { "evidence": "Expression of circulating miR-21 was significantly elevated in breast cancer patients compared to healthy women (median miR-21 expression levels were 7.67¬±2.2 and 1.28¬±0.16, respectively; p<0.0001) Patients with upregulation of circulating miR-21 were associated with poor progression-free survival (median survival 72 vs 86 weeks, respectively; log-rank (Mantel-Cox) test, p=0.049). MiR-21 expression was upregulated in breast cancer patients and might serve as a therapeutic monitoring marker." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Upregulation of Circulating MiR-21 Expression as a Potential Biomarker for Therapeutic Monitoring and Clinical Outcome in Breast Cancer.", "journal": "Asian Pacific journal of cancer prevention : APJCP", "authors": "Anwar SL, Sari DNI, Kartika AI, Fitria MS, Tanjung DS, Rakhmina D, Wardana T, Astuti I, Haryana SM, Aryandono T", "date": "2019-04-30", "evidence": [], "reference": [ { "id": "31030498", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31030498" } ] } ], "biomarker_canonical_id": "AN6531", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "c": "condition", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6532-1", "biomarker_component": [ { "biomarker": "decreased PDCD4 level", "assessed_biomarker_entity": { "recommended_name": "Programmed cell death 4", "synonyms": [ { "synonym": "H731" } ] }, "assessed_biomarker_entity_id": "NCBI:27250", "assessed_entity_type": "gene", "specimen": [ { "name": "thyroid gland", "id": "UBERON:0002046", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0002046", "loinc_code": "" } ], "evidence_source": [ { "id": "25316501", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/25316501", "evidence_list": [ { "evidence": "At enrollment, high miR-21 levels were associated with high calcitonin levels (P = .0003), lymph node metastases (P = .001), and advanced stages (P = .0003). At the end of follow-up, high miR-21 levels were associated with biochemically persistent disease (P = .0076). This study showed, in MTCs, that miR-21 regulates PDCD4 expression and also that the miR-21/PDCD4 pathway correlates with clinicopathological variables and prognosis." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0002046" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:1781", "recommended_name": { "id": "DOID:1781", "name": "thyroid gland cancer", "description": "An endocrine gland cancer located in the thryoid gland located in the neck below the thyroid cartilage.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1781" }, "synonyms": [ { "id": "DOID:1781", "name": "neoplasm of thyroid gland", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1781" }, { "id": "DOID:1781", "name": "thyroid neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1781" }, { "id": "DOID:1781", "name": "thyroid gland cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1781" }, { "id": "DOID:1781", "name": "malignant tumour of thyroid gland", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1781" }, { "id": "DOID:1781", "name": "Thyroid gland neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1781" }, { "id": "DOID:1781", "name": "malignant neoplasm of thyroid gland", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1781" } ] }, "evidence_source": [ { "id": "25316501", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/25316501", "evidence_list": [ { "evidence": "At enrollment, high miR-21 levels were associated with high calcitonin levels (P = .0003), lymph node metastases (P = .001), and advanced stages (P = .0003). At the end of follow-up, high miR-21 levels were associated with biochemically persistent disease (P = .0076). 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In contrast, the concentrations of 1,3-Dap, Put, Sp, and N-actSpd levels in serum were significantly increased in breast cancer patients." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "monitoring" } ], "condition": { "id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "name": "breast cancer", "description": "A thoracic cancer that originates in the mammary gland.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, "synonyms": [ { "id": "DOID:1612", "name": "malignant tumor of the breast", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "breast tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "mammary cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "primary breast cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "mammary tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "malignant neoplasm of breast", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" } ] }, "evidence_source": [ { "id": "17668437", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/17668437", "evidence_list": [ { "evidence": "Serum samples from 30 breast cancer patients and 30 healthy female controls were tested using the procedure described in the notes section. Breast cancer patients have higher levels of N-acetylspermidine in their blood. The serum polyamines can be a helpful method in assessing the polyamine status of breast cancer patients, as well as a strong index for studying both polyamine synthesis and metabolism. The method was used for monitoring the polyamine concentration range in urine and serum samples obtained in 30 breast cancer patients and 30 age- and gender-matched normal controls. There was no significant difference between the urine of breast cancer patients and the controls in urinary polyamine levels. In contrast, the concentrations of 1,3-Dap, Put, Sp, and N-actSpd levels in serum were significantly increased in breast cancer patients." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Analysis of polyamines as carbamoyl derivatives in urine and serum by liquid chromatography-tandem mass spectrometry.", "journal": "Biomedical chromatography : BMC", "authors": "Byun JA, Lee SH, Jung BH, Choi MH, Moon MH, Chung BC", "date": "2007-08-02", "evidence": [], "reference": [ { "id": "17668437", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/17668437" } ] } ], "biomarker_canonical_id": "AN6536", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "f": "frequency", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6537-1", "biomarker_component": [ { "biomarker": "increased GOLM1 level", "assessed_biomarker_entity": { "recommended_name": "Golgi membrane protein 1", "synonyms": [ { "synonym": "Golgi membrane protein GP73" }, { "synonym": "Golgi phosphoprotein 2" } ] }, "assessed_biomarker_entity_id": "UPKB:Q8NBJ4", "assessed_entity_type": "protein", "specimen": [ { "name": "urine", "id": "UBERON:0001088", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0001088", "loinc_code": "" } ], "evidence_source": [ { "id": "18953438", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/18953438", "evidence_list": [ { "evidence": "Our data indicating the up-regulation of GOLM1 expression and its appearance in patients' urine suggest GOLM1 as a potential novel biomarker for clinically localized prostate cancer. our group has shown that increased GOLM1 transcript in urine, along with SPINK1 and PCA3 transcript expression, and TMPRSS2:ERG fusion status were able to predict prostate cancer outcome." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0001088" } ] } ] } ], "best_biomarker_role": [ { "role": "predictive" } ], "condition": { "id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, "synonyms": [ { "id": "DOID:10283", "name": "prostate neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "NGP - new growth of prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "tumor of the prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostate cancer, familial", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostatic neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "malignant tumor of the prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "hereditary prostate cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostatic cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" } ] }, "evidence_source": [ { "id": "18953438", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/18953438", "evidence_list": [ { "evidence": "Our data indicating the up-regulation of GOLM1 expression and its appearance in patients' urine suggest GOLM1 as a potential novel biomarker for clinically localized prostate cancer. our group has shown that increased GOLM1 transcript in urine, along with SPINK1 and PCA3 transcript expression, and TMPRSS2:ERG fusion status were able to predict prostate cancer outcome." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Golgi protein GOLM1 is a tissue and urine biomarker of prostate cancer.", "journal": "Neoplasia (New York, N.Y.)", "authors": "Varambally S, Laxman B, Mehra R, Cao Q, Dhanasekaran SM, Tomlins SA, Granger J, Vellaichamy A, Sreekumar A, Yu J, Gu W, Shen R, Ghosh D, Wright LM, Kladney RD, Kuefer R, Rubin MA, Fimmel CJ, Chinnaiyan AM", "date": "2008-10-28", "evidence": [], "reference": [ { "id": "18953438", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/18953438" } ] } ], "biomarker_canonical_id": "AN6537", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "f": "frequency", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6538-1", "biomarker_component": [ { "biomarker": "increased C1GALT1 level", "assessed_biomarker_entity": { "recommended_name": "Glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase 1", "synonyms": [ { "synonym": "B3Gal-T8" }, { "synonym": "Core 1 O-glycan T-synthase" }, { "synonym": "Core 1 UDP-galactose:N-acetylgalactosamine-alpha-R beta 1,3-galactosyltransferase 1" }, { "synonym": "Beta-1,3-galactosyltransferase" }, { "synonym": "Core 1 beta1,3-galactosyltransferase 1" }, { "synonym": "C1GalT1" }, { "synonym": "Core 1 beta3-Gal-T1" } ] }, "assessed_biomarker_entity_id": "UPKB:Q9NS00", "assessed_entity_type": "protein", "specimen": [ { "name": "squamous epithelium", "id": "UBERON:0006914", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0006914", "loinc_code": "" } ], "evidence_source": [ { "id": "29930379", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/29930379", "evidence_list": [ { "evidence": "C1GALT1 expression is upregulated in HNSCC tumors and is associated with adverse clinicopathologic features. Moreover, high C1GALT1 expression predicts poor disease-free and overall survivals. For Kaplan‚ÄìMeier analysis, we further classified C1GALT1 scores 0‚Äì1 and scores 2‚Äì3 as low and high expression, respectively. Results showed that high C1GALT1 expression was significantly associated with poor disease-free survival and overall survival." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0006914" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:11934", "recommended_name": { "id": "DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11934" }, "synonyms": [ { "id": "DOID:11934", "name": "head and neck neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11934" }, { "id": "DOID:11934", "name": "head/neck neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11934" }, { "id": "DOID:11934", "name": "head and neck tumours", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11934" }, { "id": "DOID:11934", "name": "tumor of head and neck", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11934" } ] }, "evidence_source": [ { "id": "29930379", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/29930379", "evidence_list": [ { "evidence": "C1GALT1 expression is upregulated in HNSCC tumors and is associated with adverse clinicopathologic features. Moreover, high C1GALT1 expression predicts poor disease-free and overall survivals. For Kaplan‚ÄìMeier analysis, we further classified C1GALT1 scores 0‚Äì1 and scores 2‚Äì3 as low and high expression, respectively. Results showed that high C1GALT1 expression was significantly associated with poor disease-free survival and overall survival." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "C1GALT1 predicts poor prognosis and is a potential therapeutic target in head and neck cancer.", "journal": "Oncogene", "authors": "Lin MC, Chien PH, Wu HY, Chen ST, Juan HF, Lou PJ, Huang MC", "date": "2018-06-23", "evidence": [], "reference": [ { "id": "29930379", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/29930379" } ] } ], "biomarker_canonical_id": "AN6538", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "f": "frequency", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6539-1", "biomarker_component": [ { "biomarker": "Increased sIL-6R level", "assessed_biomarker_entity": { "recommended_name": "Soluble interleukin-6 receptor", "synonyms": [ { "synonym": "IL-6 receptor subunit alpha" }, { "synonym": "IL-6R subunit alpha" }, { "synonym": "IL-6R-alpha" }, { "synonym": "IL-6RA" }, { "synonym": "IL-6R 1" }, { "synonym": "Membrane glycoprotein 80" }, { "synonym": "gp80" } ] }, "assessed_biomarker_entity_id": "UPKB: P08887", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "31582665", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31582665", "evidence_list": [ { "evidence": "Among them, the serum levels of leucine-rich alpha-2-glycoprotein 1 (LRG1) were significantly different (p < 0.01) and well discriminated (area under the curve (AUC) of the receiver operating characteristic (ROC) curve >0.8) between responder and non-responder groups. The present results suggest that LRG1 and its combination with CRP and sIL-6R are promising biomarker candidates to predict response to PCRT in esophageal cancer patients." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "predictive" } ], "condition": { "id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, "synonyms": [ { "id": "DOID:5041", "name": "Ca lower third oesophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant tumor of abdominal esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "Ca middle third oesophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant neoplasm of upper third esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "esophagus cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" } ] }, "evidence_source": [ { "id": "31582665", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31582665", "evidence_list": [ { "evidence": "Among them, the serum levels of leucine-rich alpha-2-glycoprotein 1 (LRG1) were significantly different (p < 0.01) and well discriminated (area under the curve (AUC) of the receiver operating characteristic (ROC) curve >0.8) between responder and non-responder groups. The present results suggest that LRG1 and its combination with CRP and sIL-6R are promising biomarker candidates to predict response to PCRT in esophageal cancer patients." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Leucine-Rich Alpha-2-Glycoprotein 1 in Serum Is a Possible Biomarker to Predict Response to Preoperative Chemoradiotherapy for Esophageal Cancer.", "journal": "Biological & pharmaceutical bulletin", "authors": "Nambu M, Masuda T, Ito S, Kato K, Kojima T, Daiko H, Ito Y, Honda K, Ohtsuki S", "date": "2019-10-05", "evidence": [], "reference": [ { "id": "31582665", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31582665" } ] } ], "biomarker_canonical_id": "AN6539", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "f": "frequency", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6290-4", "biomarker_component": [ { "biomarker": "increased CRP level", "assessed_biomarker_entity": { "recommended_name": "C-reactive protein", "synonyms": [] }, "assessed_biomarker_entity_id": "UPKB:P02741", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "31582665", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31582665", "evidence_list": [ { "evidence": "Among them, the serum levels of leucine-rich alpha-2-glycoprotein 1 (LRG1) were significantly different (p < 0.01) and well discriminated (area under the curve (AUC) of the receiver operating characteristic (ROC) curve >0.8) between responder and non-responder groups. The present results suggest that LRG1 and its combination with CRP and sIL-6R are promising biomarker candidates to predict response to PCRT in esophageal cancer patients." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "predictive" } ], "condition": { "id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, "synonyms": [ { "id": "DOID:5041", "name": "Ca lower third oesophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant tumor of abdominal esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "Ca middle third oesophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant neoplasm of upper third esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "esophagus cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" } ] }, "evidence_source": [ { "id": "31582665", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31582665", "evidence_list": [ { "evidence": "Among them, the serum levels of leucine-rich alpha-2-glycoprotein 1 (LRG1) were significantly different (p < 0.01) and well discriminated (area under the curve (AUC) of the receiver operating characteristic (ROC) curve >0.8) between responder and non-responder groups. 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High expression at the time of diagnosis is associated with a significantly increased risk of biochemical failure." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, "synonyms": [ { "id": "DOID:10283", "name": "prostate neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "NGP - new growth of prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "tumor of the prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostate cancer, familial", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostatic neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "malignant tumor of the prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "hereditary prostate cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostatic cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" } ] }, "evidence_source": [ { "id": "15870707", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/15870707", "evidence_list": [ { "evidence": "There is a significant difference in the expression level of the 80 kDa fragment in the serum of healthy individuals vs patients with BPH and between BPH vs Loc PCA and Met PCA (P<0.001). Highest expression levels are observed in advanced metastatic disease. High expression at the time of diagnosis is associated with a significantly increased risk of biochemical failure." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Assessment of a fragment of e-cadherin as a serum biomarker with predictive value for prostate cancer.", "journal": "British journal of cancer", "authors": "Kuefer R, Hofer MD, Zorn CS, Engel O, Volkmer BG, Juarez-Brito MA, Eggel M, Gschwend JE, Rubin MA, Day ML", "date": "2005-05-05", "evidence": [], "reference": [ { "id": "15870707", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/15870707" } ] } ], "biomarker_canonical_id": "AN6543", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "c": "condition", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6544-1", "biomarker_component": [ { "biomarker": "increased CDH1 level", "assessed_biomarker_entity": { "recommended_name": "E-cadherin", "synonyms": [ { "synonym": "Arc-1" }, { "synonym": "BCDS1" }, { "synonym": "CD324" }, { "synonym": "CDHE" }, { "synonym": "ECAD" }, { "synonym": "LCAM" }, { "synonym": "UVO" } ] }, "assessed_biomarker_entity_id": "NCBI: 999", "assessed_entity_type": "gene", "specimen": [ { "name": "stomach", "id": "UBERON:0000945", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000945", "loinc_code": "21652-3" } ], "evidence_source": [ { "id": "23341533", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/23341533", "evidence_list": [ { "evidence": "CDH1 somatic alterations were found in approximately 30% of all patients with GC. CDH1 somatic alterations exist in all clinical settings and histotypes of GC and associate with different survival rates. Their screening at GC diagnosis may predict patient prognosis and is likely to improve management of patients with this disease." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000945" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" }, "synonyms": [ { "id": "DOID:10534", "name": "gastric neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" }, { "id": "DOID:10534", "name": "gastric cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" } ] }, "evidence_source": [ { "id": "23341533", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/23341533", "evidence_list": [ { "evidence": "CDH1 somatic alterations were found in approximately 30% of all patients with GC. CDH1 somatic alterations exist in all clinical settings and histotypes of GC and associate with different survival rates. Their screening at GC diagnosis may predict patient prognosis and is likely to improve management of patients with this disease." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Somatic mutations and deletions of the E-cadherin gene predict poor survival of patients with gastric cancer.", "journal": "Journal of clinical oncology : official journal of the American Society of Clinical Oncology", "authors": "Corso G, Carvalho J, Marrelli D, Vindigni C, Carvalho B, Seruca R, Roviello F, Oliveira C", "date": "2013-01-24", "evidence": [], "reference": [ { "id": "23341533", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/23341533" } ] } ], "biomarker_canonical_id": "AN6544", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6545-1", "biomarker_component": [ { "biomarker": "decreased 5HMC level", "assessed_biomarker_entity": { "recommended_name": "5-Hydroxymethylcytosine", "synonyms": [ { "synonym": "4-Amino-5-(hydroxymethyl)-2(1H)-pyrimidinone" }, { "synonym": "4-amino-5-(hydroxymethyl)pyrimidin-2(1H)-one" }, { "synonym": "5-hydroxymethylcytosine" } ] }, "assessed_biomarker_entity_id": "CHEBI:76792", "assessed_entity_type": "metabolite", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "29156615", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/29156615", "evidence_list": [ { "evidence": "When the measured levels of 5hmC2 in white blood cells were lower the patients showed significantly different distributions of prostate cancer conditions. Patients with low and elevated 5hmC content showed significantly different distributions across different prostate conditions. The distribution of these patients in prostate cancer was similar to that observed in healthy subjects, while for atypical small acinar proliferation, most patients had increased 5hmC levels. This 5hmC-based biomarker had a lower performance in the detection of prostate cancer in comparison with blood levels of prostate-specific antigen when using a cut-off point of 2.5 nanograms per milliliter. Above this threshold value, however, this biomarker allowed us to distinguish almost three-quarters of patients with prostate cancer from controls." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "monitoring" } ], "condition": { "id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, "synonyms": [ { "id": "DOID:10283", "name": "prostate neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "NGP - new growth of prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "tumor of the prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostate cancer, familial", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostatic neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "malignant tumor of the prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "hereditary prostate cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostatic cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" } ] }, "evidence_source": [ { "id": "29156615", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/29156615", "evidence_list": [ { "evidence": "When the measured levels of 5hmC2 in white blood cells were lower the patients showed significantly different distributions of prostate cancer conditions. Patients with low and elevated 5hmC content showed significantly different distributions across different prostate conditions. The distribution of these patients in prostate cancer was similar to that observed in healthy subjects, while for atypical small acinar proliferation, most patients had increased 5hmC levels. This 5hmC-based biomarker had a lower performance in the detection of prostate cancer in comparison with blood levels of prostate-specific antigen when using a cut-off point of 2.5 nanograms per milliliter. Above this threshold value, however, this biomarker allowed us to distinguish almost three-quarters of patients with prostate cancer from controls." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Clinical Significance of Measuring Global Hydroxymethylation of White Blood Cell DNA in Prostate Cancer: Comparison to PSA in a Pilot Exploratory Study.", "journal": "International journal of molecular sciences", "authors": "Grelus A, Nica DV, Miklos I, Belengeanu V, Ioiart I, Popescu C", "date": "2017-11-22", "evidence": [], "reference": [ { "id": "29156615", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/29156615" } ] } ], "biomarker_canonical_id": "AN6545", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "f": "frequency", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6546-1", "biomarker_component": [ { "biomarker": "increased ATOX1 level", "assessed_biomarker_entity": { "recommended_name": "Copper chaperone ATOX1", "synonyms": [ { "synonym": "ATX1" }, { "synonym": "HAH1" } ] }, "assessed_biomarker_entity_id": "NCBI: 475", "assessed_entity_type": "gene", "specimen": [ { "name": "breast", "id": "UBERON:0000310", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000310", "loinc_code": "" } ], "evidence_source": [ { "id": "31898157", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31898157", "evidence_list": [ { "evidence": "Since most cancer-related deaths are due to metastasis, we hypothesized that ATOX1 mRNA expression may be associated with breast cancer disease progression and thus, a prognostic biomarker in breast cancer. Our results indicate ATOX1 expression levels as a potential prognostic biomarker for ER-positive subtypes and early stages of breast cancer." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000310" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "name": "breast cancer", "description": "A thoracic cancer that originates in the mammary gland.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, "synonyms": [ { "id": "DOID:1612", "name": "malignant tumor of the breast", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "breast tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "mammary cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "primary breast cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "mammary tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "malignant neoplasm of breast", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" } ] }, "evidence_source": [ { "id": "31898157", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31898157", "evidence_list": [ { "evidence": "Since most cancer-related deaths are due to metastasis, we hypothesized that ATOX1 mRNA expression may be associated with breast cancer disease progression and thus, a prognostic biomarker in breast cancer. Our results indicate ATOX1 expression levels as a potential prognostic biomarker for ER-positive subtypes and early stages of breast cancer." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Evaluation of copper chaperone ATOX1 as prognostic biomarker in breast cancer.", "journal": "Breast cancer (Tokyo, Japan)", "authors": "Blockhuys S, Brady DC, Wittung-Stafshede P", "date": "2020-01-04", "evidence": [], "reference": [ { "id": "31898157", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31898157" } ] } ], "biomarker_canonical_id": "AN6546", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "f": "frequency", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6547-1", "biomarker_component": [ { "biomarker": "decreased MIR-193B level", "assessed_biomarker_entity": { "recommended_name": "miRNA-193b", "synonyms": [] }, "assessed_biomarker_entity_id": "MRB:MI0003137", "assessed_entity_type": "RNA", "specimen": [ { "name": "ovary", "id": "UBERON:0000992", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000992", "loinc_code": "" } ], "evidence_source": [ { "id": "26675282", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/26675282", "evidence_list": [ { "evidence": "Reduction of miR-193b was found in ovarian cancer and its lower expression was associated with poorer prognosis. Tissue miR-193b showed potential as novel biomarker for ovarian cancer. The results showed that the miR-193b expression was significantly down-regulated in ovarian cancer cell lines and tumor tissues compared with normal controls." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000992" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:2394", "recommended_name": { "id": "DOID:2394", "name": "ovarian cancer", "description": "A female reproductive organ cancer that is located_in the ovary.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, "synonyms": [ { "id": "DOID:2394", "name": "primary ovarian cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "tumor of the Ovary", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "ovary neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "malignant tumour of ovary", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "malignant Ovarian tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "ovarian neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" } ] }, "evidence_source": [ { "id": "26675282", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/26675282", "evidence_list": [ { "evidence": "Reduction of miR-193b was found in ovarian cancer and its lower expression was associated with poorer prognosis. Tissue miR-193b showed potential as novel biomarker for ovarian cancer. The results showed that the miR-193b expression was significantly down-regulated in ovarian cancer cell lines and tumor tissues compared with normal controls." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Tissue miR-193b as a Novel Biomarker for Patients with Ovarian Cancer.", "journal": "Medical science monitor : international medical journal of experimental and clinical research", "authors": "Li H, Xu Y, Qiu W, Zhao D, Zhang Y", "date": "2015-12-18", "evidence": [], "reference": [ { "id": "26675282", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/26675282" } ] } ], "biomarker_canonical_id": "AN6547", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "c": "condition", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6548-1", "biomarker_component": [ { "biomarker": "increased AFP-L3 level", "assessed_biomarker_entity": { "recommended_name": "Lectin-bound alpha-fetoprotein", "synonyms": [] }, "assessed_biomarker_entity_id": "NCIt:C96564", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "17522429", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/17522429", "evidence_list": [ { "evidence": "DCP was significantly better than total AFP and AFP-L3 in differentiating HCC from cirrhosis, with a sensitivity of 86% and specificity of 93%. All 3 markers had a lower area under the ROC curve and lower sensitivity in the group with high versus that with low risk for HCC. DCP has the best performance characteristics of all 3 serum markers for the diagnosis of HCC. Performance of all 3 biomarkers is lower in patients with high risk for HCC. 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The medians of VEGF, which was 134.96 pg/ml, levels similarly to the level of the commonly accepted tumor marker (CA 15-3 ‚Äì 25.00 U/ml) in the total group of breast cancer patients were significantly higher when compared to the healthy subjects, which is 43.40 pg/ml (p < 0.001). 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Thus, miR-613 may be useful as a prognostic marker in ovarian cancer." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000992" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:2394", "recommended_name": { "id": "DOID:2394", "name": "ovarian cancer", "description": "A female reproductive organ cancer that is located_in the ovary.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, "synonyms": [ { "id": "DOID:2394", "name": "primary ovarian cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "tumor of the Ovary", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "ovary neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "malignant tumour of ovary", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "malignant Ovarian tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "ovarian neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" } ] }, "evidence_source": [ { "id": "27010138", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/27010138", "evidence_list": [ { "evidence": "miR-613 expression in ovarian cancer tissue specimens was significantly (p < 0.001) lower than that in matched normal adjacent tissue specimens. miR-613 expression levels are low in ovarian cancer tissue and correlate with progression-free and overall survival. Thus, miR-613 may be useful as a prognostic marker in ovarian cancer." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Diminished miR-613 expression as a novel prognostic biomarker for human ovarian cancer.", "journal": "European review for medical and pharmacological sciences", "authors": "Zhang X, Zhang H", "date": "2016-03-25", "evidence": [], "reference": [ { "id": "27010138", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/27010138" } ] } ], "biomarker_canonical_id": "AN6570", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "f": "frequency", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6571-1", "biomarker_component": [ { "biomarker": "increased MIR-375-3P level", "assessed_biomarker_entity": { "recommended_name": "miRNA-375-3p", "synonyms": [] }, "assessed_biomarker_entity_id": "MRB:MI0000783", "assessed_entity_type": "RNA", "specimen": [ { "name": "esophagus", "id": "UBERON:0001043", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0001043", "loinc_code": "" } ], "evidence_source": [ { "id": "30638952", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30638952", "evidence_list": [ { "evidence": "We performed Gene Set Enrichment Analysis (GSEA) to identify the top three gene sets that significantly altered between the patients with miR-375 low expression and high expression. In conclusion, our findings suggest that miR-375 serves as a promising independent prognostic factor for ESCC and function as a tumor suppressor. patients with high miR-375 expression in ESCC had a well prognosis due to down-regulated activity of RNA polymerase I and III." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0001043" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, "synonyms": [ { "id": "DOID:5041", "name": "Ca lower third oesophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant tumor of abdominal esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "Ca middle third oesophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant neoplasm of upper third esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "esophagus cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" } ] }, "evidence_source": [ { "id": "30638952", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30638952", "evidence_list": [ { "evidence": "We performed Gene Set Enrichment Analysis (GSEA) to identify the top three gene sets that significantly altered between the patients with miR-375 low expression and high expression. In conclusion, our findings suggest that miR-375 serves as a promising independent prognostic factor for ESCC and function as a tumor suppressor. patients with high miR-375 expression in ESCC had a well prognosis due to down-regulated activity of RNA polymerase I and III." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Identification of miR-375 as a potential prognostic biomarker for esophageal squamous cell cancer: A bioinformatics analysis based on TCGA and meta-analysis.", "journal": "Pathology, research and practice", "authors": "Luo HS, Wu DH", "date": "2019-01-15", "evidence": [], "reference": [ { "id": "30638952", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30638952" } ] } ], "biomarker_canonical_id": "AN6571", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "w": "weight", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6572-1", "biomarker_component": [ { "biomarker": "increased AZGP1 level", "assessed_biomarker_entity": { "recommended_name": "Zinc alpha-2-glycoprotein", "synonyms": [ { "synonym": "Zn-alpha-2-GP" }, { "synonym": "Zn-alpha-2-glycoprotein" } ] }, "assessed_biomarker_entity_id": "UPKB:P25311", "assessed_entity_type": "protein", "specimen": [ { "name": "urine", "id": "UBERON:0001088", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0001088", "loinc_code": "" } ], "evidence_source": [ { "id": "23020913", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/23020913", "evidence_list": [ { "evidence": "Receiver operating characteristic curve analysis showed a significant predictive ability of ZAG for prostate cancer. The area under the curve (AUC) for the prediction of prostate cancer was 0.68 (95% CI 0.59-0.78) ... 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The area under the curve (AUC) for the prediction of prostate cancer was 0.68 (95% CI 0.59-0.78) ... The optimal cut-off was 1.13 for ZAG, which corresponded to 6.88 times greater odds for prostate cancer." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Zinc α2-glycoprotein as a potential novel urine biomarker for the early diagnosis of prostate cancer.", "journal": "BJU international", "authors": "Katafigiotis I, Tyritzis SI, Stravodimos KG, Alamanis C, Pavlakis K, Vlahou A, Makridakis M, Katafigioti A, Garbis SD, Constantinides CA", "date": "2012-10-02", "evidence": [], "reference": [ { "id": "23020913", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/23020913" } ] } ], "biomarker_canonical_id": "AN6572", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "c": "condition", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6573-1", "biomarker_component": [ { "biomarker": "decreased AZGP1 level", "assessed_biomarker_entity": { "recommended_name": "Zinc alpha-2-glycoprotein", "synonyms": [ { "synonym": "Zn-alpha-2-GP" }, { "synonym": "Zn-alpha-2-glycoprotein" } ] }, "assessed_biomarker_entity_id": "UPKB:P25311", "assessed_entity_type": "protein", "specimen": [ { "name": "prostate gland", "id": "UBERON:0002367", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0002367", "loinc_code": "" } ], "evidence_source": [ { "id": "28486686", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/28486686", "evidence_list": [ { "evidence": "In the phase II cohort, with a median follow-up of 15.8 years, low/absent AZGP1 expression was an independent predictor of poor BRFS (HR, 1.4; 95% CI, 1.1-1.9; P = 0.03), MFS (HR, 2.8; 95% CI, 1.2-6.6; P = 0.02) and PCSS (HR, 3.8; 95% CI, 1.5-9.5; P = 0.005). These results were validated in our prospective phase III cohort. Low/absent AZGP1 expression independently predicted for BRFS (HR, 1.9; 95% CI, 1.1-3.3; P = 0.02), with shorter MFS (HR, 2.0; 95% CI, 1.1-3.4; P = 0.02). 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These results were validated in our prospective phase III cohort. Low/absent AZGP1 expression independently predicted for BRFS (HR, 1.9; 95% CI, 1.1-3.3; P = 0.02), with shorter MFS (HR, 2.0; 95% CI, 1.1-3.4; P = 0.02). AZGP1 improved the discriminatory value when incorporated into existing prognostic risk models." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "A prospective multicentre phase III validation study of AZGP1 as a biomarker in localized prostate cancer.", "journal": "Annals of oncology : official journal of the European Society for Medical Oncology", "authors": "Zhang AY, Grogan JS, Mahon KL, Rasiah K, Sved P, Eisinger DR, Boulas J, Vasilaris A, Henshall SM, Stricker PD, Kench JG, Horvath LG", "date": "2017-05-10", "evidence": [], "reference": [ { "id": "28486686", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/28486686" } ] } ], "biomarker_canonical_id": "AN6573", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "w": "weight", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6776-1", "biomarker_component": [ { "biomarker": "Increased IFN-γ level", "assessed_biomarker_entity": { "recommended_name": "Interleukin-gamma", "synonyms": [ { "synonym": "IFN-gamma" }, { "synonym": "Immune interferon" } ] }, "assessed_biomarker_entity_id": "UPKB:P01579", "assessed_entity_type": "protein", "specimen": [ { "name": "breast", "id": "UBERON:0000310", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000310", "loinc_code": "" } ], "evidence_source": [ { "id": "31428522", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31428522", "evidence_list": [ { "evidence": "The dominant Th cytokines across all breast cancer samples were IFN-γ and IL-2. 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Th2 cytokines (IL-4, IL-5, IL-13) were expressed at low levels and not associated with any breast cancer subtype." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "A multivariate Th17 metagene for prognostic stratification in T cell non-inflamed triple negative breast cancer.", "journal": "Oncoimmunology", "authors": "Faucheux L, Grandclaudon M, Perrot-Dockès M, Sirven P, Berger F, Hamy AS, Fourchotte V, Vincent-Salomon A, Mechta-Grigoriou F, Reyal F, Scholer-Dahirel A, Guillot-Delost M, Soumelis V", "date": "2019-08-21", "evidence": [], "reference": [ { "id": "31428522", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31428522" } ] } ], "biomarker_canonical_id": "AN6776", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6576-1", "biomarker_component": [ { "biomarker": "increased Th17 level", "assessed_biomarker_entity": { "recommended_name": "T Helper cytokine 17", "synonyms": [ { "synonym": "Zn-alpha-2-GP" }, { "synonym": "Zn-alpha-2-glycoprotein" } ] }, "assessed_biomarker_entity_id": "UPKB:P25311", "assessed_entity_type": "protein", "specimen": [ { "name": "breast", "id": "UBERON:0000310", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000310", "loinc_code": "" } ], "evidence_source": [ { "id": "31428522", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31428522", "evidence_list": [ { "evidence": "Greater varieties of helper t cell can infiltrate a breast cancer microenvironment. We found that Th17, was the most favorable prognostic signature in a subset of TN breast cancer with low T cell infiltrate. We provide evidence that a Th17 signature is associated with good prognosis in TN breast cancer specifically in T-low tumors." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000310" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "name": "breast cancer", "description": "A thoracic cancer that originates in the mammary gland.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, "synonyms": [ { "id": "DOID:1612", "name": "malignant tumor of the breast", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "breast tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "mammary cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "primary breast cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "mammary tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "malignant neoplasm of breast", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" } ] }, "evidence_source": [ { "id": "31428522", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31428522", "evidence_list": [ { "evidence": "Greater varieties of helper t cell can infiltrate a breast cancer microenvironment. We found that Th17, was the most favorable prognostic signature in a subset of TN breast cancer with low T cell infiltrate. We provide evidence that a Th17 signature is associated with good prognosis in TN breast cancer specifically in T-low tumors." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "A multivariate Th17 metagene for prognostic stratification in T cell non-inflamed triple negative breast cancer.", "journal": "Oncoimmunology", "authors": "Faucheux L, Grandclaudon M, Perrot-Dockès M, Sirven P, Berger F, Hamy AS, Fourchotte V, Vincent-Salomon A, Mechta-Grigoriou F, Reyal F, Scholer-Dahirel A, Guillot-Delost M, Soumelis V", "date": "2019-08-21", "evidence": [], "reference": [ { "id": "31428522", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31428522" } ] } ], "biomarker_canonical_id": "AN6576", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "c": "condition", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6577-1", "biomarker_component": [ { "biomarker": "increased LMNB1 level", "assessed_biomarker_entity": { "recommended_name": "Lamin B1", "synonyms": [ { "synonym": "ADLD" }, { "synonym": "LMN" }, { "synonym": "LMN2" }, { "synonym": "LMNB" }, { "synonym": "MCPH26" } ] }, "assessed_biomarker_entity_id": "NCBI: 4001", "assessed_entity_type": "gene", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "19522540", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/19522540", "evidence_list": [ { "evidence": "Lamin B1 (LMNB1) mRNA was detected in 16 of 21 (76%) plasma from patients with early stage HCC and 12 of 14 (86%) from patients with late stage HCC, whereas only 19% and 17% in cirrhosis and normal subjects demonstrated LMNB1, respectively. The positivity rate of circulating LMNB1 mRNA gradually increased with tumor stages progression and it was significantly higher in HCC than in cirrhosis and normal individuals (p < 0.05 and p < 0.01, respectively). The overall detection sensitivity of LMNB1 mRNA for Hepatocellular carcinoma HCC was 80 and the specificity was 82%, where in particular for the detection of early stage and late stage HCCs the sensitivity is 76% and 86%, respectively." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:3571", "recommended_name": { "id": "DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, "synonyms": [ { "id": "DOID:3571", "name": "resectable malignant neoplasm of the liver", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "primary liver cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "Resectable malignant neoplasm of Liver", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "neoplasm of liver", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "malignant tumor of liver", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "malignant neoplasm of liver, primary", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "Ca liver - primary", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "primary malignant neoplasm of liver", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "hepatic neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "hepatic cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "malignant hepato-biliary neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" }, { "id": "DOID:3571", "name": "malignant neoplasm of liver", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_3571" } ] }, "evidence_source": [ { "id": "19522540", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/19522540", "evidence_list": [ { "evidence": "Lamin B1 (LMNB1) mRNA was detected in 16 of 21 (76%) plasma from patients with early stage HCC and 12 of 14 (86%) from patients with late stage HCC, whereas only 19% and 17% in cirrhosis and normal subjects demonstrated LMNB1, respectively. The positivity rate of circulating LMNB1 mRNA gradually increased with tumor stages progression and it was significantly higher in HCC than in cirrhosis and normal individuals (p < 0.05 and p < 0.01, respectively). The overall detection sensitivity of LMNB1 mRNA for Hepatocellular carcinoma HCC was 80 and the specificity was 82%, where in particular for the detection of early stage and late stage HCCs the sensitivity is 76% and 86%, respectively." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Circulating Lamin B1 (LMNB1) biomarker detects early stages of liver cancer in patients.", "journal": "Journal of proteome research", "authors": "Sun S, Xu MZ, Poon RT, Day PJ, Luk JM", "date": "2009-06-16", "evidence": [], "reference": [ { "id": "19522540", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/19522540" } ] } ], "biomarker_canonical_id": "AN6577", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "c": "condition", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6578-1", "biomarker_component": [ { "biomarker": "increased MKI67 level", "assessed_biomarker_entity": { "recommended_name": "KI67 antigen", "synonyms": [ { "synonym": "Antigen identified by monoclonal antibody Ki-67" }, { "synonym": "Antigen KI-67" }, { "synonym": "Antigen Ki67" } ] }, "assessed_biomarker_entity_id": "UPKB:P46013", "assessed_entity_type": "protein", "specimen": [ { "name": "breast", "id": "UBERON:0000310", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000310", "loinc_code": "" } ], "evidence_source": [ { "id": "23645542", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/23645542", "evidence_list": [ { "evidence": "The data indicated that patients whose tumors contained high levels of Ki67 effectively responded to anthracycline and taxane-containing neoadjuvant chemotherapy. Ki67 LI was a predictive marker for pCR, and all patients whose tumors achieved pathologic Complete Response (pCR) are currently disease-free." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000310" } ] } ] } ], "best_biomarker_role": [ { "role": "predictive" } ], "condition": { "id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "name": "breast cancer", "description": "A thoracic cancer that originates in the mammary gland.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, "synonyms": [ { "id": "DOID:1612", "name": "malignant tumor of the breast", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "breast tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "mammary cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "primary breast cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "mammary tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "malignant neoplasm of breast", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" } ] }, "evidence_source": [ { "id": "23645542", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/23645542", "evidence_list": [ { "evidence": "The data indicated that patients whose tumors contained high levels of Ki67 effectively responded to anthracycline and taxane-containing neoadjuvant chemotherapy. Ki67 LI was a predictive marker for pCR, and all patients whose tumors achieved pathologic Complete Response (pCR) are currently disease-free." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Prognostic significance of pathologic complete response and Ki67 expression after neoadjuvant chemotherapy in breast cancer.", "journal": "Breast cancer (Tokyo, Japan)", "authors": "Yoshioka T, Hosoda M, Yamamoto M, Taguchi K, Hatanaka KC, Takakuwa E, Hatanaka Y, Matsuno Y, Yamashita H", "date": "2013-05-07", "evidence": [], "reference": [ { "id": "23645542", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/23645542" } ] } ], "biomarker_canonical_id": "AN6578", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "c": "condition", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6579-1", "biomarker_component": [ { "biomarker": "increased AQP1 level", "assessed_biomarker_entity": { "recommended_name": "Aquaporin-1", "synonyms": [ { "synonym": "AQP-1" }, { "synonym": "Aquaporin-CHIP" }, { "synonym": "Urine water channel" }, { "synonym": "Water channel protein for red blood cells and kidney proximal tubule" } ] }, "assessed_biomarker_entity_id": "UPKB:P29972", "assessed_entity_type": "protein", "specimen": [ { "name": "urine", "id": "UBERON:0001088", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0001088", "loinc_code": "" } ], "evidence_source": [ { "id": "20375178", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/20375178", "evidence_list": [ { "evidence": "The AQP1 concentrations in patients with either clear cell or papillary carcinoma were significantly greater and clearly separated from those in the nonnephrectomy surgical control patients and the healthy individuals. High concentration of AQP1 in urine demonstrated 100% sensitivity and 100% specificity in detecting renal cancer." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0001088" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:263", "recommended_name": { "id": "DOID:263", "name": "kidney cancer", "description": "A urinary system cancer that is located_in the kidney.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_263" }, "synonyms": [ { "id": "DOID:263", "name": "malignant tumour of kidney", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_263" }, { "id": "DOID:263", "name": "malignant neoplasm of kidney except pelvis", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_263" }, { "id": "DOID:263", "name": "renal cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_263" } ] }, "evidence_source": [ { "id": "20375178", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/20375178", "evidence_list": [ { "evidence": "The AQP1 concentrations in patients with either clear cell or papillary carcinoma were significantly greater and clearly separated from those in the nonnephrectomy surgical control patients and the healthy individuals. High concentration of AQP1 in urine demonstrated 100% sensitivity and 100% specificity in detecting renal cancer." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Urinary biomarkers for the early diagnosis of kidney cancer.", "journal": "Mayo Clinic proceedings", "authors": "Morrissey JJ, London AN, Luo J, Kharasch ED", "date": "2010-04-09", "evidence": [], "reference": [ { "id": "20375178", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/20375178" } ] } ], "biomarker_canonical_id": "AN6579", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6580-1", "biomarker_component": [ { "biomarker": "increased ADFP level", "assessed_biomarker_entity": { "recommended_name": "Adipophilin", "synonyms": [ { "synonym": "Adipophilin" }, { "synonym": "Adipose differentiation-related protein" }, { "synonym": "ADRP" } ] }, "assessed_biomarker_entity_id": "UPKB:Q99541", "assessed_entity_type": "protein", "specimen": [ { "name": "urine", "id": "UBERON:0001088", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0001088", "loinc_code": "" } ], "evidence_source": [ { "id": "20375178", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/20375178", "evidence_list": [ { "evidence": "The ADFP concentrations in patients with either clear cell or papillary carcinoma were significantly greater and clearly separated from those in the nonnephrectomy surgical control patients and the healthy individuals. High ADFP concentration in the urine demonstrated 100% sensitivity and 100% specificity in detecting renal cancer." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0001088" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:263", "recommended_name": { "id": "DOID:263", "name": "kidney cancer", "description": "A urinary system cancer that is located_in the kidney.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_263" }, "synonyms": [ { "id": "DOID:263", "name": "malignant tumour of kidney", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_263" }, { "id": "DOID:263", "name": "malignant neoplasm of kidney except pelvis", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_263" }, { "id": "DOID:263", "name": "renal cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_263" } ] }, "evidence_source": [ { "id": "20375178", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/20375178", "evidence_list": [ { "evidence": "The ADFP concentrations in patients with either clear cell or papillary carcinoma were significantly greater and clearly separated from those in the nonnephrectomy surgical control patients and the healthy individuals. High ADFP concentration in the urine demonstrated 100% sensitivity and 100% specificity in detecting renal cancer." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Urinary biomarkers for the early diagnosis of kidney cancer.", "journal": "Mayo Clinic proceedings", "authors": "Morrissey JJ, London AN, Luo J, Kharasch ED", "date": "2010-04-09", "evidence": [], "reference": [ { "id": "20375178", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/20375178" } ] } ], "biomarker_canonical_id": "AN6580", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "f": "frequency", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6581-1", "biomarker_component": [ { "biomarker": "increased LACCER level", "assessed_biomarker_entity": { "recommended_name": "Lactosylceramide", "synonyms": [ { "synonym": "N-[(2S,3R,4E)-1-{[(2R,4R,5S,6R)-3,4-dihydroxy-6-(hydroxymethyl)-5-{[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxan-2-yl]oxy}-3-hydroxyoctadec-4-en-2-yl]dodecanamide" }, { "synonym": "Lactosylceramide" }, { "synonym": "1-O-(4-O-beta-delta-Galactopyranosyl-beta-glucopyranosyl)ceramide" }, { "synonym": "LacCer(d18:1/12:0)" }, { "synonym": "1-O-(4-O-beta-delta-Galactopyranosyl-beta-delta-glucopyranosyl)-Ceramide" }, { "synonym": "beta-delta-Galactosyl-1,4-beta-delta-Glucosylceramide" }, { "synonym": "CDH" }, { "synonym": "1-O-(4-O-b-D-Galactopyranosyl-b-D-glucopyranosyl)-Ceramide" }, { "synonym": "N-Lignoceryl sphingosyl lactoside" }, { "synonym": "Gal-beta1->4Glc-beta1->1'Cer" }, { "synonym": "delta-Galactosyl-1,4-beta-delta-glucosylceramide" }, { "synonym": "D-Galactosyl-1,4-beta-D-glucosylceramide" }, { "synonym": "1ylce-O-(4-O-beta-delta-Galactopyranosyl-beta-glucopyranosyl)ceramide" }, { "synonym": "LacCer" }, { "synonym": "Lactosyl-N-acylsphingosine" }, { "synonym": "N-(Dodecanoyl)-1-b-lactosyl-sphing-4-enine" }, { "synonym": "Cytolipin H" }, { "synonym": "CDw17 antigen" }, { "synonym": "beta-D-Galactosyl-1,4-beta-D-Glucosylceramide" }, { "synonym": "N-(Dodecanoyl)-1-beta-lactosyl-sphing-4-enine" }, { "synonym": "1-O-(4-O-beta-D-Galactopyranosyl-beta-glucopyranosyl)ceramide" }, { "synonym": "Lactosyl ceramide (d18:1/12:0)" }, { "synonym": "beta-delta-Galactosyl-1,4-beta-delta-glucosramide" } ] }, "assessed_biomarker_entity_id": "CHEBI:89446", "assessed_entity_type": "metabolite", "specimen": [ { "name": "urine", "id": "UBERON:0001088", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0001088", "loinc_code": "" } ], "evidence_source": [ { "id": "27914242", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/27914242", "evidence_list": [ { "evidence": "In terms of lipid classes, it was noted that HexCer species were in general more abundant in urinary exosomes from prostate cancer patients than from healthy controls, and that LacCer species were increased or unchanged. This is an interesting result since antibodies against LacCer and GlcCer are available, opening the alternative of analyzing these lipids by antibody-based methods, which are widely used in clinical laboratories. LacCer also showed the highest patient-to-control ratio." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0001088" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, "synonyms": [ { "id": "DOID:10283", "name": "prostate neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "NGP - new growth of prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "tumor of the prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostate cancer, familial", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostatic neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "malignant tumor of the prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "hereditary prostate cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostatic cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" } ] }, "evidence_source": [ { "id": "27914242", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/27914242", "evidence_list": [ { "evidence": "In terms of lipid classes, it was noted that HexCer species were in general more abundant in urinary exosomes from prostate cancer patients than from healthy controls, and that LacCer species were increased or unchanged. This is an interesting result since antibodies against LacCer and GlcCer are available, opening the alternative of analyzing these lipids by antibody-based methods, which are widely used in clinical laboratories. LacCer also showed the highest patient-to-control ratio." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Molecular lipid species in urinary exosomes as potential prostate cancer biomarkers.", "journal": "European journal of cancer (Oxford, England : 1990)", "authors": "Skotland T, Ekroos K, Kauhanen D, Simolin H, Seierstad T, Berge V, Sandvig K, Llorente A", "date": "2016-12-04", "evidence": [], "reference": [ { "id": "27914242", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/27914242" } ] } ], "biomarker_canonical_id": "AN6581", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "w": "weight", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6582-1", "biomarker_component": [ { "biomarker": "increased HEXCER level", "assessed_biomarker_entity": { "recommended_name": "Hexosylceramide", "synonyms": [ { "synonym": "N-hexadecanoyl hexosylceramide" }, { "synonym": "HexCer d18:1/16:0" }, { "synonym": "N-hexadecanoyl-(1<->1)-hexosyl-sphing-4-enine" } ] }, "assessed_biomarker_entity_id": "CHEBI:77462", "assessed_entity_type": "metabolite", "specimen": [ { "name": "urine", "id": "UBERON:0001088", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0001088", "loinc_code": "" } ], "evidence_source": [ { "id": "27914242", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/27914242", "evidence_list": [ { "evidence": "It was noted that HexCer species were in general more abundant in urinary exosomes from prostate cancer patients than from healthy controls, and that LacCer species were increased or unchanged." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0001088" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, "synonyms": [ { "id": "DOID:10283", "name": "prostate neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "NGP - new growth of prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "tumor of the prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostate cancer, familial", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostatic neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "malignant tumor of the prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "hereditary prostate cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostatic cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" } ] }, "evidence_source": [ { "id": "27914242", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/27914242", "evidence_list": [ { "evidence": "It was noted that HexCer species were in general more abundant in urinary exosomes from prostate cancer patients than from healthy controls, and that LacCer species were increased or unchanged." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Molecular lipid species in urinary exosomes as potential prostate cancer biomarkers.", "journal": "European journal of cancer (Oxford, England : 1990)", "authors": "Skotland T, Ekroos K, Kauhanen D, Simolin H, Seierstad T, Berge V, Sandvig K, Llorente A", "date": "2016-12-04", "evidence": [], "reference": [ { "id": "27914242", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/27914242" } ] } ], "biomarker_canonical_id": "AN6582", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6583-1", "biomarker_component": [ { "biomarker": "decreased PS level", "assessed_biomarker_entity": { "recommended_name": "Phosphatidylserine", "synonyms": [ { "synonym": "PS(18:1/18:1)" } ] }, "assessed_biomarker_entity_id": "CHEBI:90437", "assessed_entity_type": "metabolite", "specimen": [ { "name": "urine", "id": "UBERON:0001088", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0001088", "loinc_code": "" } ], "evidence_source": [ { "id": "27914242", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/27914242", "evidence_list": [ { "evidence": "PS 18:1/18:1 alone demonstrated lower expression in urine in patients as compared to the controls. Also, the author calculated that in urinary exosomes, PS 18:0e18:1 in the inner leaflet could occupy 72 18% (mean SD; n Z 13) and 66 22% (mean SD; n Z 15) of the area occupied by long-chain sphingolipids (N amidated C22 and C24) in urinary exosomes from controls and prostate cancer patients, respectively. The highest significance was shown for phosphatidylserine (PS) 18:1/18:1 and lactosylceramide (d18:1/16:0), the latter also showed the highest patient-to-control ratio. Furthermore, combinations of these lipid species and PS 18:0-18:2 distinguished the two groups with 93% sensitivity and 100% specificity." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0001088" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, "synonyms": [ { "id": "DOID:10283", "name": "prostate neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "NGP - new growth of prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "tumor of the prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostate cancer, familial", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostatic neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "malignant tumor of the prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "hereditary prostate cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostatic cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" } ] }, "evidence_source": [ { "id": "27914242", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/27914242", "evidence_list": [ { "evidence": "PS 18:1/18:1 alone demonstrated lower expression in urine in patients as compared to the controls. Also, the author calculated that in urinary exosomes, PS 18:0e18:1 in the inner leaflet could occupy 72 18% (mean SD; n Z 13) and 66 22% (mean SD; n Z 15) of the area occupied by long-chain sphingolipids (N amidated C22 and C24) in urinary exosomes from controls and prostate cancer patients, respectively. The highest significance was shown for phosphatidylserine (PS) 18:1/18:1 and lactosylceramide (d18:1/16:0), the latter also showed the highest patient-to-control ratio. Furthermore, combinations of these lipid species and PS 18:0-18:2 distinguished the two groups with 93% sensitivity and 100% specificity." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Molecular lipid species in urinary exosomes as potential prostate cancer biomarkers.", "journal": "European journal of cancer (Oxford, England : 1990)", "authors": "Skotland T, Ekroos K, Kauhanen D, Simolin H, Seierstad T, Berge V, Sandvig K, Llorente A", "date": "2016-12-04", "evidence": [], "reference": [ { "id": "27914242", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/27914242" } ] } ], "biomarker_canonical_id": "AN6583", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6584-1", "biomarker_component": [ { "biomarker": "Increased ADIRF level", "assessed_biomarker_entity": { "recommended_name": "Adipogenesis regulatory factor", "synonyms": [ { "synonym": "Adipogenesis factor rich in obesity" }, { "synonym": "Adipose most abundant gene transcript 2 protein" }, { "synonym": "Adipose-specific protein 2" }, { "synonym": "apM-2" } ] }, "assessed_biomarker_entity_id": "UPKB:Q15847", "assessed_entity_type": "protein", "specimen": [ { "name": "urine", "id": "UBERON:0001088", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0001088", "loinc_code": "" } ], "evidence_source": [ { "id": "26196085", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/26196085", "evidence_list": [ { "evidence": "TM256 and LAMTOR1 could be used to augment the sensitivity to 100%. Other prominent proteins were V-type proton ATPase 16 kDa proteolipid subunit (VATL), adipogenesis regulatory factor (ADIRF), and several Rab-class members and proteasomal proteins." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0001088" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, "synonyms": [ { "id": "DOID:10283", "name": "prostate neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "NGP - new growth of prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "tumor of the prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostate cancer, familial", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostatic neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "malignant tumor of the prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "hereditary prostate cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostatic cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" } ] }, "evidence_source": [ { "id": "26196085", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/26196085", "evidence_list": [ { "evidence": "TM256 and LAMTOR1 could be used to augment the sensitivity to 100%. Other prominent proteins were V-type proton ATPase 16 kDa proteolipid subunit (VATL), adipogenesis regulatory factor (ADIRF), and several Rab-class members and proteasomal proteins." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Identification of prostate cancer biomarkers in urinary exosomes.", "journal": "Oncotarget", "authors": "Øverbye A, Skotland T, Koehler CJ, Thiede B, Seierstad T, Berge V, Sandvig K, Llorente A", "date": "2015-07-22", "evidence": [], "reference": [ { "id": "26196085", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/26196085" } ] } ], "biomarker_canonical_id": "AN6584", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "f": "frequency", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6585-1", "biomarker_component": [ { "biomarker": "Increased VATL level", "assessed_biomarker_entity": { "recommended_name": "V-type proton ATPase 16 kDa proteolipid subunit", "synonyms": [ { "synonym": "V-ATPase 16 kDa proteolipid subunit c" }, { "synonym": "Vacuolar proton pump 16 kDa proteolipid subunit c" } ] }, "assessed_biomarker_entity_id": "UPKB:P27449", "assessed_entity_type": "protein", "specimen": [ { "name": "urine", "id": "UBERON:0001088", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0001088", "loinc_code": "" } ], "evidence_source": [ { "id": "26196085", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/26196085", "evidence_list": [ { "evidence": "TM256 and LAMTOR1 could be used to augment the sensitivity to 100%. Other prominent proteins were V-type proton ATPase 16 kDa proteolipid subunit (VATL), adipogenesis regulatory factor (ADIRF), and several Rab-class members and proteasomal proteins." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0001088" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, "synonyms": [ { "id": "DOID:10283", "name": "prostate neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "NGP - new growth of prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "tumor of the prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostate cancer, familial", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostatic neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "malignant tumor of the prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "hereditary prostate cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostatic cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" } ] }, "evidence_source": [ { "id": "26196085", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/26196085", "evidence_list": [ { "evidence": "TM256 and LAMTOR1 could be used to augment the sensitivity to 100%. Other prominent proteins were V-type proton ATPase 16 kDa proteolipid subunit (VATL), adipogenesis regulatory factor (ADIRF), and several Rab-class members and proteasomal proteins." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Identification of prostate cancer biomarkers in urinary exosomes.", "journal": "Oncotarget", "authors": "Øverbye A, Skotland T, Koehler CJ, Thiede B, Seierstad T, Berge V, Sandvig K, Llorente A", "date": "2015-07-22", "evidence": [], "reference": [ { "id": "26196085", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/26196085" } ] } ], "biomarker_canonical_id": "AN6585", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "w": "weight", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6586-1", "biomarker_component": [ { "biomarker": "Increased LAMTOR1 level", "assessed_biomarker_entity": { "recommended_name": "Late endosomal/lysosomal adaptor, MAPK and MTOR activator 1", "synonyms": [ { "synonym": "Late endosomal/lysosomal adaptor and MAPK and MTOR activator 1" }, { "synonym": "Lipid raft adaptor protein p18" }, { "synonym": "Protein associated with DRMs and endosomes" }, { "synonym": "p27Kip1-releasing factor from RhoA" }, { "synonym": "p27RF-Rho" } ] }, "assessed_biomarker_entity_id": "UPKB:Q6IAA8", "assessed_entity_type": "protein", "specimen": [ { "name": "urine", "id": "UBERON:0001088", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0001088", "loinc_code": "" } ], "evidence_source": [ { "id": "26196085", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/26196085", "evidence_list": [ { "evidence": "The most interesting potential prostate cancer biomarker identified in our study (both at 100% specificity and combined specificity and sensitivity) is TM256/C17orf61, a protein that has been predicted to be located at the plasma membrane and in exosomes. TM256 showed the highest sensitivity (94%) and level of enrichment (140-fold) of all the detected proteins. The fact that TM256 is also relatively abundant in patient exosomes further increases the interest for this protein as a promising biomarker." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0001088" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, "synonyms": [ { "id": "DOID:10283", "name": "prostate neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "NGP - new growth of prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "tumor of the prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostate cancer, familial", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostatic neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "malignant tumor of the prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "hereditary prostate cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostatic cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" } ] }, "evidence_source": [ { "id": "26196085", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/26196085", "evidence_list": [ { "evidence": "The most interesting potential prostate cancer biomarker identified in our study (both at 100% specificity and combined specificity and sensitivity) is TM256/C17orf61, a protein that has been predicted to be located at the plasma membrane and in exosomes. TM256 showed the highest sensitivity (94%) and level of enrichment (140-fold) of all the detected proteins. The fact that TM256 is also relatively abundant in patient exosomes further increases the interest for this protein as a promising biomarker." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Identification of prostate cancer biomarkers in urinary exosomes.", "journal": "Oncotarget", "authors": "Øverbye A, Skotland T, Koehler CJ, Thiede B, Seierstad T, Berge V, Sandvig K, Llorente A", "date": "2015-07-22", "evidence": [], "reference": [ { "id": "26196085", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/26196085" } ] } ], "biomarker_canonical_id": "AN6586", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6587-1", "biomarker_component": [ { "biomarker": "increased TM256 level", "assessed_biomarker_entity": { "recommended_name": "Transmembrane protein 256", "synonyms": [] }, "assessed_biomarker_entity_id": "UPKB:Q8N2U0", "assessed_entity_type": "protein", "specimen": [ { "name": "urine", "id": "UBERON:0001088", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0001088", "loinc_code": "" } ], "evidence_source": [ { "id": "26196085", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/26196085", "evidence_list": [ { "evidence": "The most interesting potential prostate cancer biomarker identified in our study (both at 100% specificity and combined specificity and sensitivity) is TM256/C17orf61, a protein that has been predicted to be located at the plasma membrane and in exosomes. TM256 showed the highest sensitivity (94%) and level of enrichment (140-fold) of all the detected proteins. The fact that TM256 is also relatively abundant in patient exosomes further increases the interest for this protein as a promising biomarker." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0001088" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, "synonyms": [ { "id": "DOID:10283", "name": "prostate neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "NGP - new growth of prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "tumor of the prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostate cancer, familial", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostatic neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "malignant tumor of the prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "hereditary prostate cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostatic cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" } ] }, "evidence_source": [ { "id": "26196085", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/26196085", "evidence_list": [ { "evidence": "The most interesting potential prostate cancer biomarker identified in our study (both at 100% specificity and combined specificity and sensitivity) is TM256/C17orf61, a protein that has been predicted to be located at the plasma membrane and in exosomes. TM256 showed the highest sensitivity (94%) and level of enrichment (140-fold) of all the detected proteins. The fact that TM256 is also relatively abundant in patient exosomes further increases the interest for this protein as a promising biomarker." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Identification of prostate cancer biomarkers in urinary exosomes.", "journal": "Oncotarget", "authors": "Øverbye A, Skotland T, Koehler CJ, Thiede B, Seierstad T, Berge V, Sandvig K, Llorente A", "date": "2015-07-22", "evidence": [], "reference": [ { "id": "26196085", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/26196085" } ] } ], "biomarker_canonical_id": "AN6587", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "c": "condition", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6588-1", "biomarker_component": [ { "biomarker": "increased FKBP4 level", "assessed_biomarker_entity": { "recommended_name": "Peptidyl-prolyl cis-trans isomerase", "synonyms": [ { "synonym": "PPIase FKBP4" }, { "synonym": "51 kDa FK506-binding protein" }, { "synonym": "FKBP51" }, { "synonym": "52 kDa FK506-binding protein" }, { "synonym": "52 kDa FKBP" }, { "synonym": "FKBP-52" }, { "synonym": "59 kDa immunophilin" }, { "synonym": "p59" }, { "synonym": "FK506-binding protein 4" }, { "synonym": "FKBP-4" }, { "synonym": "FKBP59" }, { "synonym": "HSP-binding immunophilin" }, { "synonym": "HBI" }, { "synonym": "Immunophilin FKBP52" }, { "synonym": "Rotamase" } ] }, "assessed_biomarker_entity_id": "UPKB:Q02790", "assessed_entity_type": "protein", "specimen": [ { "name": "prostate gland", "id": "UBERON:0002367", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0002367", "loinc_code": "" } ], "evidence_source": [ { "id": "17722004", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/17722004", "evidence_list": [ { "evidence": "FKBP4 was increased in PCa specimen. It was also interesting that FKBP4 (also known as FKBP52) was up-regulated in Pca." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0002367" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, "synonyms": [ { "id": "DOID:10283", "name": "prostate neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "NGP - new growth of prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "tumor of the prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostate cancer, familial", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostatic neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "malignant tumor of the prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "hereditary prostate cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostatic cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" } ] }, "evidence_source": [ { "id": "17722004", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/17722004", "evidence_list": [ { "evidence": "FKBP4 was increased in PCa specimen. It was also interesting that FKBP4 (also known as FKBP52) was up-regulated in Pca." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Identification of candidate prostate cancer biomarkers in prostate needle biopsy specimens using proteomic analysis.", "journal": "International journal of cancer", "authors": "Lin JF, Xu J, Tian HY, Gao X, Chen QX, Gu Q, Xu GJ, Song JD, Zhao FK", "date": "2007-08-28", "evidence": [], "reference": [ { "id": "17722004", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/17722004" } ] } ], "biomarker_canonical_id": "AN6588", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "f": "frequency", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6589-1", "biomarker_component": [ { "biomarker": "decreased FLNA level", "assessed_biomarker_entity": { "recommended_name": "Filamin-A", "synonyms": [ { "synonym": "FLN-A" }, { "synonym": "Actin-binding protein 280" }, { "synonym": "ABP-280" }, { "synonym": "Alpha-filamin" }, { "synonym": "Endothelial actin-binding protein" }, { "synonym": "Filamin-1" }, { "synonym": "Non-muscle filamin" } ] }, "assessed_biomarker_entity_id": "UPKB:P21333", "assessed_entity_type": "protein", "specimen": [ { "name": "prostate gland", "id": "UBERON:0002367", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0002367", "loinc_code": "" } ], "evidence_source": [ { "id": "17722004", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/17722004", "evidence_list": [ { "evidence": "2-DE protein profile of FLNA(7‚Äì15) clearly reveals a decrease in this protein in PNBX specimens from PCa patients. FLNA(7‚Äì15) levels were notably reduced in AMACR-positive PCa specimens as measured by immunoblot analysis (Fig. 3e). These results, taken with proteomics observations, suggest that FLNA(7‚Äì15) is down-regulated in prostate cancer. Among the proteins identified, the most notable was the endogenous 100-kDa fragment of FLNA and FKBP4, FLNA(7‚Äì15), which was found to be markedly down-regulated in PCa specimens." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0002367" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, "synonyms": [ { "id": "DOID:10283", "name": "prostate neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "NGP - new growth of prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "tumor of the prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostate cancer, familial", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostatic neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "malignant tumor of the prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "hereditary prostate cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostatic cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" } ] }, "evidence_source": [ { "id": "17722004", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/17722004", "evidence_list": [ { "evidence": "2-DE protein profile of FLNA(7‚Äì15) clearly reveals a decrease in this protein in PNBX specimens from PCa patients. FLNA(7‚Äì15) levels were notably reduced in AMACR-positive PCa specimens as measured by immunoblot analysis (Fig. 3e). These results, taken with proteomics observations, suggest that FLNA(7‚Äì15) is down-regulated in prostate cancer. Among the proteins identified, the most notable was the endogenous 100-kDa fragment of FLNA and FKBP4, FLNA(7‚Äì15), which was found to be markedly down-regulated in PCa specimens." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Identification of candidate prostate cancer biomarkers in prostate needle biopsy specimens using proteomic analysis.", "journal": "International journal of cancer", "authors": "Lin JF, Xu J, Tian HY, Gao X, Chen QX, Gu Q, Xu GJ, Song JD, Zhao FK", "date": "2007-08-28", "evidence": [], "reference": [ { "id": "17722004", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/17722004" } ] } ], "biomarker_canonical_id": "AN6589", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "f": "frequency", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6590-1", "biomarker_component": [ { "biomarker": "increased MYO5A level", "assessed_biomarker_entity": { "recommended_name": "Unconventional myosin-Va", "synonyms": [ { "synonym": "Dilute myosin heavy chain, non-muscle" }, { "synonym": "Myosin heavy chain 12" }, { "synonym": "Myosin-12" }, { "synonym": "Myoxin" } ] }, "assessed_biomarker_entity_id": "UPKB:Q9Y4I1", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "30532555", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30532555", "evidence_list": [ { "evidence": "On the bottom left is the WASF1 module which included MYO5A and WASF1. 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These two genes both interacted with NCKAP1, CYFIP2, and CYFIP1. In this WASF1 module, four genes (CYFIP1, CYFIP2, NCKAP1, and WASF1) were involved in hsa04810: regulation of actin cytoskeleton. It has been reported that actin cytoskeleton was associated with lung cancer migration and invasion" } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Identification of tumor-educated platelet biomarkers of non-small-cell lung cancer.", "journal": "OncoTargets and therapy", "authors": "Sheng M, Dong Z, Xie Y", "date": "2018-12-12", "evidence": [], "reference": [ { "id": "30532555", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30532555" } ] } ], "biomarker_canonical_id": "AN6591", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "w": "weight", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6592-1", "biomarker_component": [ { "biomarker": "increased PDHB level", "assessed_biomarker_entity": { "recommended_name": "Pyruvate dehydrogenase E1 component subunit beta, mitochondrial", "synonyms": [ { "synonym": "PDHE1-B" } ] }, "assessed_biomarker_entity_id": "UPKB:P11177", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "30532555", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30532555", "evidence_list": [ { "evidence": "The PDHB module, which was involved in carbohydrate metabolism. The PDHB module interacted with the RSRC1 module, which was associated with protein biosynthesis, growth, and migration. These biomarkers can accurately predict NSCLC. In-depth biological network analysis suggested that there were four modules and three intermodule hubs that may trigger NSCLC" } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "predictive" } ], "condition": { "id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1324" }, "synonyms": [] }, "evidence_source": [ { "id": "30532555", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30532555", "evidence_list": [ { "evidence": "The PDHB module, which was involved in carbohydrate metabolism. The PDHB module interacted with the RSRC1 module, which was associated with protein biosynthesis, growth, and migration. These biomarkers can accurately predict NSCLC. In-depth biological network analysis suggested that there were four modules and three intermodule hubs that may trigger NSCLC" } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Identification of tumor-educated platelet biomarkers of non-small-cell lung cancer.", "journal": "OncoTargets and therapy", "authors": "Sheng M, Dong Z, Xie Y", "date": "2018-12-12", "evidence": [], "reference": [ { "id": "30532555", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30532555" } ] } ], "biomarker_canonical_id": "AN6592", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "c": "condition", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6593-1", "biomarker_component": [ { "biomarker": "increased RSRC1 level", "assessed_biomarker_entity": { "recommended_name": "Serine/arginine-related protein 53", "synonyms": [ { "synonym": "BM-011" }, { "synonym": "MRT70" }, { "synonym": "SFRS21" }, { "synonym": "SRrp53" } ] }, "assessed_biomarker_entity_id": "NCBI: 51319", "assessed_entity_type": "gene", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "30532555", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30532555", "evidence_list": [ { "evidence": "At the top middle was the RSRC1 module, which included RSRC1 and FLOT1. Within this module, eight genes (RPS11, RPS14, RPS15, RPS26, RPS28, RPS3, RPS3A, and RPS9) that RSRC1 interacted with were ribosomal protein genes. Ribosome is important for protein biosynthesis, and there have been several reports that downregulation of ribosomal protein can inhibit or attenuate NSCLC growth and migration." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "monitoring" } ], "condition": { "id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1324" }, "synonyms": [] }, "evidence_source": [ { "id": "30532555", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30532555", "evidence_list": [ { "evidence": "At the top middle was the RSRC1 module, which included RSRC1 and FLOT1. Within this module, eight genes (RPS11, RPS14, RPS15, RPS26, RPS28, RPS3, RPS3A, and RPS9) that RSRC1 interacted with were ribosomal protein genes. Ribosome is important for protein biosynthesis, and there have been several reports that downregulation of ribosomal protein can inhibit or attenuate NSCLC growth and migration." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Identification of tumor-educated platelet biomarkers of non-small-cell lung cancer.", "journal": "OncoTargets and therapy", "authors": "Sheng M, Dong Z, Xie Y", "date": "2018-12-12", "evidence": [], "reference": [ { "id": "30532555", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30532555" } ] } ], "biomarker_canonical_id": "AN6593", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "c": "condition", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6594-1", "biomarker_component": [ { "biomarker": "increased methylation IN PITX2", "assessed_biomarker_entity": { "recommended_name": "Pituitary homeobox 2 gene methylation", "synonyms": [ { "synonym": "ARP1" }, { "synonym": "ASGD4" }, { "synonym": "Brx1" }, { "synonym": "IDG2" }, { "synonym": "IGDS" }, { "synonym": "IGDS2" }, { "synonym": "IHG2" }, { "synonym": "IRID2" }, { "synonym": "Otlx2" }, { "synonym": "PTX2" }, { "synonym": "RGS" }, { "synonym": "RIEG" }, { "synonym": "RIEG1" }, { "synonym": "RS" } ] }, "assessed_biomarker_entity_id": "NCBI: 5308", "assessed_entity_type": "gene", "specimen": [ { "name": "prostate gland", "id": "UBERON:0002367", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0002367", "loinc_code": "" } ], "evidence_source": [ { "id": "25402584", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/25402584", "evidence_list": [ { "evidence": "However, after FDR adjustment at 5% was applied, only methylation of PITX2 remained significant (p = 0.005) for predicting PCa related death and is interpreted as the following: for each 10% increase in methylation of PITX2, the risk of PCa-related death increased by a factor of 1.56." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0002367" } ] } ] } ], "best_biomarker_role": [ { "role": "predictive" } ], "condition": { "id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, "synonyms": [ { "id": "DOID:10283", "name": "prostate neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "NGP - new growth of prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "tumor of the prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostate cancer, familial", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostatic neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "malignant tumor of the prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "hereditary prostate cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostatic cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" } ] }, "evidence_source": [ { "id": "25402584", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/25402584", "evidence_list": [ { "evidence": "However, after FDR adjustment at 5% was applied, only methylation of PITX2 remained significant (p = 0.005) for predicting PCa related death and is interpreted as the following: for each 10% increase in methylation of PITX2, the risk of PCa-related death increased by a factor of 1.56." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "DNA methylation of PITX2 predicts poor survival in men with prostate cancer.", "journal": "Biomarkers in medicine", "authors": "Vasiljević N, Ahmad AS, Carter PD, Fisher G, Berney DM, Foster CS, Cuzick J, Lorincz AT", "date": "2014-11-18", "evidence": [], "reference": [ { "id": "25402584", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/25402584" } ] } ], "biomarker_canonical_id": "AN6594", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6595-1", "biomarker_component": [ { "biomarker": "increased CXCR4 level", "assessed_biomarker_entity": { "recommended_name": "C-X-C chemokine receptor type 4", "synonyms": [ { "synonym": "CXC-R4" }, { "synonym": "CXCR-4" }, { "synonym": "FB22" }, { "synonym": "Fusin" }, { "synonym": "HM89" }, { "synonym": "LCR1" }, { "synonym": "Leukocyte-derived seven transmembrane domain receptor" }, { "synonym": "LESTR" }, { "synonym": "Lipopolysaccharide-associated protein 3" }, { "synonym": "LAP-3" }, { "synonym": "LPS-associated protein 3" }, { "synonym": "NPYRL" }, { "synonym": "Stromal cell-derived factor 1 receptor" }, { "synonym": "SDF-1 receptor" } ] }, "assessed_biomarker_entity_id": "UPKB:P61073", "assessed_entity_type": "protein", "specimen": [ { "name": "skin epidermis", "id": "UBERON:0001003", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0001003", "loinc_code": "" } ], "evidence_source": [ { "id": "15756007", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/15756007", "evidence_list": [ { "evidence": "The CXCR4 expression on tumor cells was correlated with an unfavorable prognosis with a median disease-free and overall survival of 22 and 35 months, respectively. The hazard ratios of relapse and death, compared with patients with CXCR4-negative tumors, were 2.5 (95% confidence interval, 1.2-6.1) and 3.1 (95% confidence interval, 1.1-7.2), respectively. This article provides the first evidence that CXCR4 expression could be an independent and powerful prognostic marker in primary cutaneous malignant melanomas." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0001003" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_4159" }, "synonyms": [ { "id": "DOID:4159", "name": "CA - skin cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_4159" }, { "id": "DOID:4159", "name": "malignant neoplasm of skin", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_4159" }, { "id": "DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_4159" } ] }, "evidence_source": [ { "id": "15756007", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/15756007", "evidence_list": [ { "evidence": "The CXCR4 expression on tumor cells was correlated with an unfavorable prognosis with a median disease-free and overall survival of 22 and 35 months, respectively. The hazard ratios of relapse and death, compared with patients with CXCR4-negative tumors, were 2.5 (95% confidence interval, 1.2-6.1) and 3.1 (95% confidence interval, 1.1-7.2), respectively. This article provides the first evidence that CXCR4 expression could be an independent and powerful prognostic marker in primary cutaneous malignant melanomas." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Expression of CXCR4 predicts poor prognosis in patients with malignant melanoma.", "journal": "Clinical cancer research : an official journal of the American Association for Cancer Research", "authors": "Scala S, Ottaiano A, Ascierto PA, Cavalli M, Simeone E, Giuliano P, Napolitano M, Franco R, Botti G, Castello G", "date": "2005-03-10", "evidence": [], "reference": [ { "id": "15756007", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/15756007" } ] } ], "biomarker_canonical_id": "AN6595", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "f": "frequency", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6372-3", "biomarker_component": [ { "biomarker": "increased IL8 level", "assessed_biomarker_entity": { "recommended_name": "Interleukin-8", "synonyms": [ { "synonym": "IL-8" }, { "synonym": "C-X-C motif chemokine 8" }, { "synonym": "Chemokine (C-X-C motif) ligand 8" }, { "synonym": "Emoctakin" }, { "synonym": "Granulocyte chemotactic protein 1" }, { "synonym": "GCP-1" }, { "synonym": "Monocyte-derived neutrophil chemotactic factor" }, { "synonym": "MDNCF" }, { "synonym": "Monocyte-derived neutrophil-activating peptide" }, { "synonym": "MONAP" }, { "synonym": "Neutrophil-activating protein 1" }, { "synonym": "NAP-1" }, { "synonym": "Protein 3-10C" }, { "synonym": "T-cell chemotactic factor" } ] }, "assessed_biomarker_entity_id": "UPKB:P10145", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "33211-4" } ], "evidence_source": [ { "id": "21673904", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/21673904", "evidence_list": [ { "evidence": "We have shown that, after the elimination of serum interference, IL-8 and cathepsin B were significantly elevated in melanoma." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_4159" }, "synonyms": [ { "id": "DOID:4159", "name": "CA - skin cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_4159" }, { "id": "DOID:4159", "name": "malignant neoplasm of skin", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_4159" }, { "id": "DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_4159" } ] }, "evidence_source": [ { "id": "21673904", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/21673904", "evidence_list": [ { "evidence": "We have shown that, after the elimination of serum interference, IL-8 and cathepsin B were significantly elevated in melanoma." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "IL-8 and cathepsin B as melanoma serum biomarkers.", "journal": "International journal of molecular sciences", "authors": "Zhang H, Fu T, McGettigan S, Kumar S, Liu S, Speicher D, Schuchter L, Xu X", "date": "2011-06-16", "evidence": [], "reference": [ { "id": "21673904", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/21673904" } ] } ], "biomarker_canonical_id": "AN6372", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "f": "frequency", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6596-1", "biomarker_component": [ { "biomarker": "increased CTSB level", "assessed_biomarker_entity": { "recommended_name": "Cathepsin B", "synonyms": [ { "synonym": "APP secretase" }, { "synonym": "APPS" }, { "synonym": "Cathepsin B1" } ] }, "assessed_biomarker_entity_id": "UPKB:P07858", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "21673904", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/21673904", "evidence_list": [ { "evidence": "Indeed, significantly elevated levels of Cathepsin B (as determined by unpaired t test) were observed in melanoma patients. However, Cathepsin B levels were also elevated in breast cancer patients, indicating that cathepsin B is not unique to melanoma but may be associated with general tumor progression. Cathepsin B levels were also independent of age and stages of melanoma. In our study, serum cathepsin B levels were elevated in both melanoma and breast cancer patients. Based on these data, it is suggested that cathepsin B might be relevant to the development of a broad range of tumor, possibly contributing to the tumor cell migration and metastasis due to its protease function." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_4159" }, "synonyms": [ { "id": "DOID:4159", "name": "CA - skin cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_4159" }, { "id": "DOID:4159", "name": "malignant neoplasm of skin", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_4159" }, { "id": "DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_4159" } ] }, "evidence_source": [ { "id": "21673904", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/21673904", "evidence_list": [ { "evidence": "Indeed, significantly elevated levels of Cathepsin B (as determined by unpaired t test) were observed in melanoma patients. However, Cathepsin B levels were also elevated in breast cancer patients, indicating that cathepsin B is not unique to melanoma but may be associated with general tumor progression. Cathepsin B levels were also independent of age and stages of melanoma. In our study, serum cathepsin B levels were elevated in both melanoma and breast cancer patients. Based on these data, it is suggested that cathepsin B might be relevant to the development of a broad range of tumor, possibly contributing to the tumor cell migration and metastasis due to its protease function." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "IL-8 and cathepsin B as melanoma serum biomarkers.", "journal": "International journal of molecular sciences", "authors": "Zhang H, Fu T, McGettigan S, Kumar S, Liu S, Speicher D, Schuchter L, Xu X", "date": "2011-06-16", "evidence": [], "reference": [ { "id": "21673904", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/21673904" } ] } ], "biomarker_canonical_id": "AN6596", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "f": "frequency", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6597-1", "biomarker_component": [ { "biomarker": "Increased LPHN3 level", "assessed_biomarker_entity": { "recommended_name": "Latrophilin 3", "synonyms": [ { "synonym": "CIRL3" }, { "synonym": "CL3" }, { "synonym": "LEC3" }, { "synonym": "LPHN3" } ] }, "assessed_biomarker_entity_id": "NCBI:23284", "assessed_entity_type": "gene", "specimen": [ { "name": "prostate gland", "id": "UBERON:0002367", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0002367", "loinc_code": "" } ], "evidence_source": [ { "id": "29861410", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/29861410", "evidence_list": [ { "evidence": "The dominant Th cytokines across all breast cancer samples were IFN-γ and IL-2. 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"resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" } ] }, "evidence_source": [ { "id": "31570444", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31570444", "evidence_list": [ { "evidence": "Low MLH1 expression was associated with improved prognosis and is a possible predictor of the chemosensitivity of ovarian cancer." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "MLH1 Is a Prognostic Biomarker for Serous Ovarian Cancer Treated With Platinum- and Taxane-based Chemotherapy.", "journal": "Anticancer research", "authors": "Kawashima N, Yoshida H, Miwa M, Fujiwara K", "date": "2019-10-02", "evidence": [], "reference": [ { "id": "31570444", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31570444" } ] } ], "biomarker_canonical_id": "AN6602", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6603-1", "biomarker_component": [ { "biomarker": "Increased HAPLN3 Promoter Hypermethylation", "assessed_biomarker_entity": { "recommended_name": "Hyaluronan And Proteoglycan Link Protein 3", "synonyms": [ { "synonym": "EXLD1" }, { "synonym": "HsT19883" } ] }, "assessed_biomarker_entity_id": "NCBI:145864", "assessed_entity_type": "gene", "specimen": [ { "name": "prostate gland", "id": "UBERON:0002367", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0002367", "loinc_code": "" } ], "evidence_source": [ { "id": "29465788", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/29465788", "evidence_list": [ { "evidence": "Moreover, as proof of principle, we successfully detected highly PC-specific hypermethylated circulating tumor DNA (ctDNA) for ST6GALNAC3, ZNF660, HAPLN3, and CCDC181 in liquid biopsies (serum) from 27 patients with PC vs. 10 patients with BPH, using droplet digital methylation-specific PCR analysis. Finally, we generated a three-gene (ST6GALNAC3/CCDC181/HAPLN3) ctDNA hypermethylation model, which detected PC with 100% specificity and 67% sensitivity." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0002367" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, "synonyms": [ { "id": "DOID:10283", "name": "prostate neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "NGP - new growth of prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "tumor of the prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostate cancer, familial", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostatic neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "malignant tumor of the prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "hereditary prostate cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostatic cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" } ] }, "evidence_source": [ { "id": "29465788", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/29465788", "evidence_list": [ { "evidence": "Moreover, as proof of principle, we successfully detected highly PC-specific hypermethylated circulating tumor DNA (ctDNA) for ST6GALNAC3, ZNF660, HAPLN3, and CCDC181 in liquid biopsies (serum) from 27 patients with PC vs. 10 patients with BPH, using droplet digital methylation-specific PCR analysis. Finally, we generated a three-gene (ST6GALNAC3/CCDC181/HAPLN3) ctDNA hypermethylation model, which detected PC with 100% specificity and 67% sensitivity." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Biomarker potential of ST6GALNAC3 and ZNF660 promoter hypermethylation in prostate cancer tissue and liquid biopsies.", "journal": "Molecular oncology", "authors": "Haldrup C, Pedersen AL, Øgaard N, Strand SH, Høyer S, Borre M, Ørntoft TF, Sørensen KD", "date": "2018-02-22", "evidence": [], "reference": [ { "id": "29465788", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/29465788" } ] } ], "biomarker_canonical_id": "AN6603", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "f": "frequency", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6604-1", "biomarker_component": [ { "biomarker": "Increased CCDC181 Promoter Hypermethylation", "assessed_biomarker_entity": { "recommended_name": "Coiled-Coil Domain Containing 181", "synonyms": [ { "synonym": "C1orf114" } ] }, "assessed_biomarker_entity_id": "NCBI:57821", "assessed_entity_type": "gene", "specimen": [ { "name": "prostate gland", "id": "UBERON:0002367", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0002367", "loinc_code": "" } ], "evidence_source": [ { "id": "29465788", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/29465788", "evidence_list": [ { "evidence": "Moreover, as proof of principle, we successfully detected highly PC-specific hypermethylated circulating tumor DNA (ctDNA) for ST6GALNAC3, ZNF660, HAPLN3, and CCDC181 in liquid biopsies (serum) from 27 patients with PC vs. 10 patients with BPH, using droplet digital methylation-specific PCR analysis. Finally, we generated a three-gene (ST6GALNAC3/CCDC181/HAPLN3) ctDNA hypermethylation model, which detected PC with 100% specificity and 67% sensitivity." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0002367" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, "synonyms": [ { "id": "DOID:10283", "name": "prostate neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "NGP - new growth of prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "tumor of the prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostate cancer, familial", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostatic neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "malignant tumor of the prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "hereditary prostate cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostatic cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" } ] }, "evidence_source": [ { "id": "29465788", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/29465788", "evidence_list": [ { "evidence": "Moreover, as proof of principle, we successfully detected highly PC-specific hypermethylated circulating tumor DNA (ctDNA) for ST6GALNAC3, ZNF660, HAPLN3, and CCDC181 in liquid biopsies (serum) from 27 patients with PC vs. 10 patients with BPH, using droplet digital methylation-specific PCR analysis. Finally, we generated a three-gene (ST6GALNAC3/CCDC181/HAPLN3) ctDNA hypermethylation model, which detected PC with 100% specificity and 67% sensitivity." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Biomarker potential of ST6GALNAC3 and ZNF660 promoter hypermethylation in prostate cancer tissue and liquid biopsies.", "journal": "Molecular oncology", "authors": "Haldrup C, Pedersen AL, Øgaard N, Strand SH, Høyer S, Borre M, Ørntoft TF, Sørensen KD", "date": "2018-02-22", "evidence": [], "reference": [ { "id": "29465788", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/29465788" } ] } ], "biomarker_canonical_id": "AN6604", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "c": "condition", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6605-1", "biomarker_component": [ { "biomarker": "decreased ZNF660 level", "assessed_biomarker_entity": { "recommended_name": "Zinc finger protein 660", "synonyms": [] }, "assessed_biomarker_entity_id": "NCBI: 285349", "assessed_entity_type": "gene", "specimen": [ { "name": "prostate gland", "id": "UBERON:0002367", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0002367", "loinc_code": "" } ], "evidence_source": [ { "id": "29465788", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/29465788", "evidence_list": [ { "evidence": "We furthermore identify ZNF660 hypermethylation as associated with increased risk of BCR, as well as with reduced OS and reduced CSS, thus showing promising prognostic potential. ZNF660 hypermethylation was also significantly associated with poor overall and PC-specific survival in the RP." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0002367" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, "synonyms": [ { "id": "DOID:10283", "name": "prostate neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "NGP - new growth of prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "tumor of the prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostate cancer, familial", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostatic neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "malignant tumor of the prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "hereditary prostate cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostatic cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" } ] }, "evidence_source": [ { "id": "29465788", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/29465788", "evidence_list": [ { "evidence": "We furthermore identify ZNF660 hypermethylation as associated with increased risk of BCR, as well as with reduced OS and reduced CSS, thus showing promising prognostic potential. ZNF660 hypermethylation was also significantly associated with poor overall and PC-specific survival in the RP." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Biomarker potential of ST6GALNAC3 and ZNF660 promoter hypermethylation in prostate cancer tissue and liquid biopsies.", "journal": "Molecular oncology", "authors": "Haldrup C, Pedersen AL, Øgaard N, Strand SH, Høyer S, Borre M, Ørntoft TF, Sørensen KD", "date": "2018-02-22", "evidence": [], "reference": [ { "id": "29465788", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/29465788" } ] } ], "biomarker_canonical_id": "AN6605", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "c": "condition", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6606-1", "biomarker_component": [ { "biomarker": "decreased ST6GALNAC3 level", "assessed_biomarker_entity": { "recommended_name": "Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 3", "synonyms": [ { "synonym": "SIAT7-F" }, { "synonym": "SIAT7F" }, { "synonym": "ST6GALNACVI" } ] }, "assessed_biomarker_entity_id": "NCBI: 30815", "assessed_entity_type": "gene", "specimen": [ { "name": "prostate gland", "id": "UBERON:0002367", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0002367", "loinc_code": "" } ], "evidence_source": [ { "id": "29465788", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/29465788", "evidence_list": [ { "evidence": "ST6GALNAC3 and ZNF660 mRNA levels were significantly downregulated in PC compared to AN tissue samples (P < 0.0001; Fig. 1K,L). Furthermore, the mRNA expression level of each gene was moderately, but significantly, inversely correlated with the promoter methylation level (P < 0.001; Fig. 1M,N), collectively suggesting that aberrant promoter hypermethylation may contribute to downregulation of ST6GALNAC3 and ZNF660 in PC." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0002367" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, "synonyms": [ { "id": "DOID:10283", "name": "prostate neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "NGP - new growth of prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "tumor of the prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostate cancer, familial", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostatic neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "malignant tumor of the prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "hereditary prostate cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostatic cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" } ] }, "evidence_source": [ { "id": "29465788", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/29465788", "evidence_list": [ { "evidence": "ST6GALNAC3 and ZNF660 mRNA levels were significantly downregulated in PC compared to AN tissue samples (P < 0.0001; Fig. 1K,L). Furthermore, the mRNA expression level of each gene was moderately, but significantly, inversely correlated with the promoter methylation level (P < 0.001; Fig. 1M,N), collectively suggesting that aberrant promoter hypermethylation may contribute to downregulation of ST6GALNAC3 and ZNF660 in PC." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Biomarker potential of ST6GALNAC3 and ZNF660 promoter hypermethylation in prostate cancer tissue and liquid biopsies.", "journal": "Molecular oncology", "authors": "Haldrup C, Pedersen AL, Øgaard N, Strand SH, Høyer S, Borre M, Ørntoft TF, Sørensen KD", "date": "2018-02-22", "evidence": [], "reference": [ { "id": "29465788", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/29465788" } ] } ], "biomarker_canonical_id": "AN6606", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "c": "condition", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6607-1", "biomarker_component": [ { "biomarker": "increased XPO6 level", "assessed_biomarker_entity": { "recommended_name": "Exportin-6", "synonyms": [ { "synonym": "EXP6" }, { "synonym": "RANBP20" } ] }, "assessed_biomarker_entity_id": "NCBI: 23214", "assessed_entity_type": "gene", "specimen": [ { "name": "prostate gland", "id": "UBERON:0002367", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0002367", "loinc_code": "" } ], "evidence_source": [ { "id": "26709895", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/26709895", "evidence_list": [ { "evidence": "XPO6 expression was significantly higher in patients with elevated PSA levels (>20 ng/ml) prior to radical prostatectomy (P=0.02). Elevated XPO6 expression was also found in patients with higher combined Gleason score (>/=8) in both biopsy and radical prostatectomy specimens (P=1.34E-3, P=3.09E-3, respectively). Furthermore, a positive association was found for the elevated expression of XPO6 and lymph node metastasis occurrence (P=0.01), biochemical recurrence (P=1.57E-3), and distant metastasis occurrence (P=3.27E-4)." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0002367" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, "synonyms": [ { "id": "DOID:10283", "name": "prostate neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "NGP - new growth of prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "tumor of the prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostate cancer, familial", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostatic neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "malignant tumor of the prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "hereditary prostate cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostatic cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" } ] }, "evidence_source": [ { "id": "26709895", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/26709895", "evidence_list": [ { "evidence": "XPO6 expression was significantly higher in patients with elevated PSA levels (>20 ng/ml) prior to radical prostatectomy (P=0.02). Elevated XPO6 expression was also found in patients with higher combined Gleason score (>/=8) in both biopsy and radical prostatectomy specimens (P=1.34E-3, P=3.09E-3, respectively). Furthermore, a positive association was found for the elevated expression of XPO6 and lymph node metastasis occurrence (P=0.01), biochemical recurrence (P=1.57E-3), and distant metastasis occurrence (P=3.27E-4)." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Elevated XPO6 expression as a potential prognostic biomarker for prostate cancer recurrence.", "journal": "Frontiers in bioscience (Scholar edition)", "authors": "Hao J, Chiang YT, Gout PW, Wang Y", "date": "2015-12-29", "evidence": [], "reference": [ { "id": "26709895", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/26709895" } ] } ], "biomarker_canonical_id": "AN6607", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6608-1", "biomarker_component": [ { "biomarker": "decreased ZFP36 level", "assessed_biomarker_entity": { "recommended_name": "Tristetraprolin", "synonyms": [ { "synonym": "G0S24" }, { "synonym": "GOS24" }, { "synonym": "NUP475" }, { "synonym": "RNF162A" }, { "synonym": "TIS11" }, { "synonym": "TTP" }, { "synonym": "zfp-36" } ] }, "assessed_biomarker_entity_id": "NCBI: 7538", "assessed_entity_type": "gene", "specimen": [ { "name": "prostate gland", "id": "UBERON:0002367", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0002367", "loinc_code": "" } ], "evidence_source": [ { "id": "30420441", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30420441", "evidence_list": [ { "evidence": "Lower levels of tristetraprolin in human prostate cancer prostatectomy tissue are associated with more aggressive prostate cancer and may serve as an actionable prognostic and predictive biomarker." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0002367" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, "synonyms": [ { "id": "DOID:10283", "name": "prostate neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "NGP - new growth of prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "tumor of the prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostate cancer, familial", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostatic neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "malignant tumor of the prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "hereditary prostate cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostatic cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" } ] }, "evidence_source": [ { "id": "30420441", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30420441", "evidence_list": [ { "evidence": "Lower levels of tristetraprolin in human prostate cancer prostatectomy tissue are associated with more aggressive prostate cancer and may serve as an actionable prognostic and predictive biomarker." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Low Tristetraprolin Expression Is Associated with Lethal Prostate Cancer.", "journal": "Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology", "authors": "Gerke T, Beltran H, Wang X, Lee GM, Sboner A, Karnes RJ, Klein EA, Davicioni E, Yousefi K, Ross AE, Börnigen D, Huttenhower C, Mucci LA, Trock BJ, Sweeney CJ", "date": "2018-11-14", "evidence": [], "reference": [ { "id": "30420441", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30420441" } ] } ], "biomarker_canonical_id": "AN6608", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "w": "weight", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6609-1", "biomarker_component": [ { "biomarker": "increased EZH2 level", "assessed_biomarker_entity": { "recommended_name": "Zeste homolog 2", "synonyms": [ { "synonym": "ENX-1" }, { "synonym": "Enhancer of zeste homolog 2" }, { "synonym": "Lysine N-methyltransferase 6" } ] }, "assessed_biomarker_entity_id": "UPKB:Q15910", "assessed_entity_type": "protein", "specimen": [ { "name": "prostate gland", "id": "UBERON:0002367", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0002367", "loinc_code": "96964-2" } ], "evidence_source": [ { "id": "12374981", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/12374981", "evidence_list": [ { "evidence": "EZH2 protein are increased in metastatic prostate cancer; in addition, clinically localized prostate cancers that express higher concentrations of EZH2 show a poorer prognosis. Thus, dysregulated expression of EZH2 may be involved in the progression of prostate cancer, as well as being a marker that distinguishes indolent prostate cancer from those at risk of lethal Progression." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0002367" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, "synonyms": [ { "id": "DOID:10283", "name": "prostate neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "NGP - new growth of prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "tumor of the prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostate cancer, familial", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostatic neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "malignant tumor of the prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "hereditary prostate cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostatic cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" } ] }, "evidence_source": [ { "id": "12374981", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/12374981", "evidence_list": [ { "evidence": "EZH2 protein are increased in metastatic prostate cancer; in addition, clinically localized prostate cancers that express higher concentrations of EZH2 show a poorer prognosis. Thus, dysregulated expression of EZH2 may be involved in the progression of prostate cancer, as well as being a marker that distinguishes indolent prostate cancer from those at risk of lethal Progression." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "The polycomb group protein EZH2 is involved in progression of prostate cancer.", "journal": "Nature", "authors": "Varambally S, Dhanasekaran SM, Zhou M, Barrette TR, Kumar-Sinha C, Sanda MG, Ghosh D, Pienta KJ, Sewalt RG, Otte AP, Rubin MA, Chinnaiyan AM", "date": "2002-10-11", "evidence": [], "reference": [ { "id": "12374981", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/12374981" } ] } ], "biomarker_canonical_id": "AN6609", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "f": "frequency", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6610-1", "biomarker_component": [ { "biomarker": "increased FABP4 level", "assessed_biomarker_entity": { "recommended_name": "Fatty acid-binding protein, adipocyte", "synonyms": [ { "synonym": "Adipocyte lipid-binding protein" }, { "synonym": "ALBP" }, { "synonym": "Adipocyte-type fatty acid-binding protein" }, { "synonym": "A-FABP" }, { "synonym": "AFABP" }, { "synonym": "Fatty acid-binding protein 4" } ] }, "assessed_biomarker_entity_id": "UPKB:P15090", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "30100196", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30100196", "evidence_list": [ { "evidence": "Using clinical samples, we demonstrated that circulating A-FABP levels were significantly increased in obese patients with breast cancer in comparison with those without breast cancer. Collectively, these data suggest circulating A-FABP as a new link between obesity and breast cancer risk, thereby revealing A-FABP as a potential new therapeutic target for treatment of obesity-associated cancers." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "risk" } ], "condition": { "id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "name": "breast cancer", "description": "A thoracic cancer that originates in the mammary gland.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, "synonyms": [ { "id": "DOID:1612", "name": "malignant tumor of the breast", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "breast tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "mammary cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "primary breast cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "mammary tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "malignant neoplasm of breast", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" } ] }, "evidence_source": [ { "id": "30100196", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30100196", "evidence_list": [ { "evidence": "Using clinical samples, we demonstrated that circulating A-FABP levels were significantly increased in obese patients with breast cancer in comparison with those without breast cancer. Collectively, these data suggest circulating A-FABP as a new link between obesity and breast cancer risk, thereby revealing A-FABP as a potential new therapeutic target for treatment of obesity-associated cancers." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Circulating Adipose Fatty Acid Binding Protein Is a New Link Underlying Obesity-Associated Breast/Mammary Tumor Development.", "journal": "Cell metabolism", "authors": "Hao J, Zhang Y, Yan X, Yan F, Sun Y, Zeng J, Waigel S, Yin Y, Fraig MM, Egilmez NK, Suttles J, Kong M, Liu S, Cleary MP, Sauter E, Li B", "date": "2018-08-14", "evidence": [], "reference": [ { "id": "30100196", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30100196" } ] } ], "biomarker_canonical_id": "AN6610", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "f": "frequency", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6611-1", "biomarker_component": [ { "biomarker": "increased ENG level", "assessed_biomarker_entity": { "recommended_name": "Endoglin", "synonyms": [] }, "assessed_biomarker_entity_id": "UPKB:P17813", "assessed_entity_type": "protein", "specimen": [ { "name": "urine", "id": "UBERON:0001088", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0001088", "loinc_code": "" } ], "evidence_source": [ { "id": "19004009", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/19004009", "evidence_list": [ { "evidence": "Elevations in post-DRE urinary endoglin suggest there may be value in further studying endoglin as a urinary biomarker of prostate cancer. Endoglin levels in both urine and serum may aid in prostate cancer detection and prognostication. In the present study, we show that endoglin is increased in urine collected after DRE from men with prostate cancer on biopsy compared to men without prostate cancer, and that post-DRE urinary endoglin levels are predictive of prostate cancer in a cohort of men at increased risk by PSA and DRE criteria." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0001088" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, "synonyms": [ { "id": "DOID:10283", "name": "prostate neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "NGP - new growth of prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "tumor of the prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostate cancer, familial", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostatic neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "malignant tumor of the prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "hereditary prostate cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostatic cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" } ] }, "evidence_source": [ { "id": "19004009", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/19004009", "evidence_list": [ { "evidence": "Elevations in post-DRE urinary endoglin suggest there may be value in further studying endoglin as a urinary biomarker of prostate cancer. Endoglin levels in both urine and serum may aid in prostate cancer detection and prognostication. In the present study, we show that endoglin is increased in urine collected after DRE from men with prostate cancer on biopsy compared to men without prostate cancer, and that post-DRE urinary endoglin levels are predictive of prostate cancer in a cohort of men at increased risk by PSA and DRE criteria." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Endoglin (CD105) as a urinary and serum marker of prostate cancer.", "journal": "International journal of cancer", "authors": "Fujita K, Ewing CM, Chan DY, Mangold LA, Partin AW, Isaacs WB, Pavlovich CP", "date": "2008-11-13", "evidence": [], "reference": [ { "id": "19004009", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/19004009" } ] } ], "biomarker_canonical_id": "AN6611", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "c": "condition", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6612-1", "biomarker_component": [ { "biomarker": "increased AMACR level", "assessed_biomarker_entity": { "recommended_name": "Alpha-methylacyl-CoA racemase", "synonyms": [ { "synonym": "2-methylacyl-CoA racemase" } ] }, "assessed_biomarker_entity_id": "UPKB:Q9UHK6", "assessed_entity_type": "protein", "specimen": [ { "name": "urine", "id": "UBERON:0001088", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0001088", "loinc_code": "" } ], "evidence_source": [ { "id": "15371879", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/15371879", "evidence_list": [ { "evidence": "AMACR was detected in the urine in 18 of 26 patients (69%). AMACR was detected in all 12 patients with biopsy confirmed adenocarcinoma of the prostate (100 sensitivity, 95% CI 75 to 100), in 5 of 12 with no evidence of cancer on biopsy (58% specificity, 95% CI 29 to 78) and in 1 of 2 (50%, 95% CI 3 to 80) with atypia on biopsy. Overall AMACR detection was associated with cancer status by prostate biopsy in 21 of 26 patients (86%). A screening test based on urinary AMACR may develop into a useful adjunct to serum prostate specific antigen and digital rectal examination for identifying men at increased risk for harboring prostate cancer despite negative biopsy. Such a test has potential application for stratifying patients into low and high risk groups for surveillance vs repeat biopsy." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0001088" } ] } ] } ], "best_biomarker_role": [ { "role": "risk" } ], "condition": { "id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, "synonyms": [ { "id": "DOID:10283", "name": "prostate neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "NGP - new growth of prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "tumor of the prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostate cancer, familial", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostatic neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "malignant tumor of the prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "hereditary prostate cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostatic cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" } ] }, "evidence_source": [ { "id": "15371879", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/15371879", "evidence_list": [ { "evidence": "AMACR was detected in the urine in 18 of 26 patients (69%). AMACR was detected in all 12 patients with biopsy confirmed adenocarcinoma of the prostate (100 sensitivity, 95% CI 75 to 100), in 5 of 12 with no evidence of cancer on biopsy (58% specificity, 95% CI 29 to 78) and in 1 of 2 (50%, 95% CI 3 to 80) with atypia on biopsy. Overall AMACR detection was associated with cancer status by prostate biopsy in 21 of 26 patients (86%). A screening test based on urinary AMACR may develop into a useful adjunct to serum prostate specific antigen and digital rectal examination for identifying men at increased risk for harboring prostate cancer despite negative biopsy. Such a test has potential application for stratifying patients into low and high risk groups for surveillance vs repeat biopsy." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Prostate cancer detection on urinalysis for alpha methylacyl coenzyme a racemase protein.", "journal": "The Journal of urology", "authors": "Rogers CG, Yan G, Zha S, Gonzalgo ML, Isaacs WB, Luo J, De Marzo AM, Nelson WG, Pavlovich CP", "date": "2004-09-17", "evidence": [], "reference": [ { "id": "15371879", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/15371879" } ] } ], "biomarker_canonical_id": "AN6612", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "w": "weight", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6613-1", "biomarker_component": [ { "biomarker": "increased IMPDH2 level", "assessed_biomarker_entity": { "recommended_name": "Inosine 5'-monophosphate dehydrogenase type II", "synonyms": [ { "synonym": "IMP dehydrogenase 2" }, { "synonym": "IMPD 2" }, { "synonym": "IMPDH 2" }, { "synonym": "Inosine-5'-monophosphate dehydrogenase type II" }, { "synonym": "IMP dehydrogenase II" }, { "synonym": "IMPDH-II" } ] }, "assessed_biomarker_entity_id": "UPKB:P12268", "assessed_entity_type": "protein", "specimen": [ { "name": "ovary", "id": "UBERON:0000992", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000992", "loinc_code": "" } ], "evidence_source": [ { "id": "32305001", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32305001", "evidence_list": [ { "evidence": "IMPDH2 is highly expressed in ovarian cancer and correlates with prognosis, which may serve as a potential prognostic biomarker." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000992" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:2394", "recommended_name": { "id": "DOID:2394", "name": "ovarian cancer", "description": "A female reproductive organ cancer that is located_in the ovary.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, "synonyms": [ { "id": "DOID:2394", "name": "primary ovarian cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "tumor of the Ovary", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "ovary neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "malignant tumour of ovary", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "malignant Ovarian tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "ovarian neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" } ] }, "evidence_source": [ { "id": "32305001", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32305001", "evidence_list": [ { "evidence": "IMPDH2 is highly expressed in ovarian cancer and correlates with prognosis, which may serve as a potential prognostic biomarker." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "The expression and prognostic role of IMPDH2 in ovarian cancer.", "journal": "Annals of diagnostic pathology", "authors": "Tian Y, Zhang J, Chen L, Zhang X", "date": "2020-04-19", "evidence": [], "reference": [ { "id": "32305001", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32305001" } ] } ], "biomarker_canonical_id": "AN6613", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6614-1", "biomarker_component": [ { "biomarker": "increased MIR-106A-5P level", "assessed_biomarker_entity": { "recommended_name": "miRNA-106a-5p", "synonyms": [] }, "assessed_biomarker_entity_id": "MRB:MIMAT0000103", "assessed_entity_type": "RNA", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "26276721", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/26276721", "evidence_list": [ { "evidence": "miR-106a-5p was found to be significantly (p < 0.05) upregulated in BC tissue samples compared to paired adjacent healthy tissue samples." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "name": "breast cancer", "description": "A thoracic cancer that originates in the mammary gland.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, "synonyms": [ { "id": "DOID:1612", "name": "malignant tumor of the breast", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "breast tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "mammary cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "primary breast cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "mammary tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "malignant neoplasm of breast", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" } ] }, "evidence_source": [ { "id": "26276721", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/26276721", "evidence_list": [ { "evidence": "miR-106a-5p was found to be significantly (p < 0.05) upregulated in BC tissue samples compared to paired adjacent healthy tissue samples." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Circulating miRNAs revealed as surrogate molecular signatures for the early detection of breast cancer.", "journal": "Cancer letters", "authors": "Mishra S, Srivastava AK, Suman S, Kumar V, Shukla Y", "date": "2015-08-16", "evidence": [], "reference": [ { "id": "26276721", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/26276721" } ] } ], "biomarker_canonical_id": "AN6614", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "f": "frequency", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6615-1", "biomarker_component": [ { "biomarker": "decreased MIR-495 level", "assessed_biomarker_entity": { "recommended_name": "miRNA-495", "synonyms": [] }, "assessed_biomarker_entity_id": "MRB:MI0003135", "assessed_entity_type": "RNA", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "26276721", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/26276721", "evidence_list": [ { "evidence": "Results showed differential pattern of expressions of these miRNAs in multiple cohorts, however in early stage breast cancer, miR-106a-5p and miR-454-3p were upregulated (p < 0.05), miR-195-5p and miR-495 were downregulated (p < 0.05) in PBMCs. In addition, these miRNAs were also significantly associated with cancer and ErbB signaling pathways. The present study delineated the importance of miR-195-5p and miR-495 miRNAs as prospective circulating surrogate molecular signatures for early detection of breast cancer." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "name": "breast cancer", "description": "A thoracic cancer that originates in the mammary gland.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, "synonyms": [ { "id": "DOID:1612", "name": "malignant tumor of the breast", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "breast tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "mammary cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "primary breast cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "mammary tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "malignant neoplasm of breast", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" } ] }, "evidence_source": [ { "id": "26276721", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/26276721", "evidence_list": [ { "evidence": "Results showed differential pattern of expressions of these miRNAs in multiple cohorts, however in early stage breast cancer, miR-106a-5p and miR-454-3p were upregulated (p < 0.05), miR-195-5p and miR-495 were downregulated (p < 0.05) in PBMCs. In addition, these miRNAs were also significantly associated with cancer and ErbB signaling pathways. The present study delineated the importance of miR-195-5p and miR-495 miRNAs as prospective circulating surrogate molecular signatures for early detection of breast cancer." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Circulating miRNAs revealed as surrogate molecular signatures for the early detection of breast cancer.", "journal": "Cancer letters", "authors": "Mishra S, Srivastava AK, Suman S, Kumar V, Shukla Y", "date": "2015-08-16", "evidence": [], "reference": [ { "id": "26276721", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/26276721" } ] } ], "biomarker_canonical_id": "AN6615", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "c": "condition", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6616-1", "biomarker_component": [ { "biomarker": "increased MIR-454-3P level", "assessed_biomarker_entity": { "recommended_name": "miRNA-454-3p", "synonyms": [] }, "assessed_biomarker_entity_id": "MRB:MIMAT0003885", "assessed_entity_type": "RNA", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "26276721", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/26276721", "evidence_list": [ { "evidence": "Results showed differential pattern of expressions of these miRNAs in multiple cohorts, however in early stage breast cancer, miR-106a-5p and miR-454-3p were upregulated (p < 0.05), miR-195-5p and miR-495 were downregulated (p < 0.05) in PBMCs. In addition, these miRNAs were also significantly associated with cancer and ErbB signaling pathways." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "name": "breast cancer", "description": "A thoracic cancer that originates in the mammary gland.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, "synonyms": [ { "id": "DOID:1612", "name": "malignant tumor of the breast", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "breast tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "mammary cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "primary breast cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "mammary tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "malignant neoplasm of breast", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" } ] }, "evidence_source": [ { "id": "26276721", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/26276721", "evidence_list": [ { "evidence": "Results showed differential pattern of expressions of these miRNAs in multiple cohorts, however in early stage breast cancer, miR-106a-5p and miR-454-3p were upregulated (p < 0.05), miR-195-5p and miR-495 were downregulated (p < 0.05) in PBMCs. In addition, these miRNAs were also significantly associated with cancer and ErbB signaling pathways." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Circulating miRNAs revealed as surrogate molecular signatures for the early detection of breast cancer.", "journal": "Cancer letters", "authors": "Mishra S, Srivastava AK, Suman S, Kumar V, Shukla Y", "date": "2015-08-16", "evidence": [], "reference": [ { "id": "26276721", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/26276721" } ] } ], "biomarker_canonical_id": "AN6616", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "c": "condition", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6617-1", "biomarker_component": [ { "biomarker": "decreased MIR-195-5P level", "assessed_biomarker_entity": { "recommended_name": "miRNA-195-5p", "synonyms": [] }, "assessed_biomarker_entity_id": "MRB:MIMAT0000461", "assessed_entity_type": "RNA", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "32259560", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32259560", "evidence_list": [ { "evidence": "In early stage breast cancer, miR-106a-5p and miR-454-3p were upregulated (p < 0.05), miR-195-5p and miR-495 were downregulated (p < 0.05) in PBMCs. Results showed differential pattern of expressions of these miRNAs in multiple cohorts, however in early stage breast cancer, miR-106a-5p and miR-454-3p were upregulated (p < 0.05), miR-195-5p and miR-495 were downregulated (p < 0.05) in PBMCs. In addition, these miRNAs were also significantly associated with cancer and ErbB signaling pathways." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "name": "COVID-19", "description": "A thoracic cancer that originates in the mammary gland.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, "synonyms": [ { "id": "DOID:1612", "name": "malignant tumor of the breast", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "breast tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "mammary cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "primary breast cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "mammary tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "malignant neoplasm of breast", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" } ] }, "evidence_source": [ { "id": "32259560", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32259560", "evidence_list": [ { "evidence": "In early stage breast cancer, miR-106a-5p and miR-454-3p were upregulated (p < 0.05), miR-195-5p and miR-495 were downregulated (p < 0.05) in PBMCs. Results showed differential pattern of expressions of these miRNAs in multiple cohorts, however in early stage breast cancer, miR-106a-5p and miR-454-3p were upregulated (p < 0.05), miR-195-5p and miR-495 were downregulated (p < 0.05) in PBMCs. 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Wang X, Xie Y, Wang Z, Xu Y, You X, Liang Z, Cao H", "date": "2015-06-03", "evidence": [], "reference": [ { "id": "26033707", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/26033707" } ] } ], "biomarker_canonical_id": "AN6628", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "f": "frequency", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6629-1", "biomarker_component": [ { "biomarker": "increased LNCRNA H19 level", "assessed_biomarker_entity": { "recommended_name": "Long non-coding RNA H19", "synonyms": [] }, "assessed_biomarker_entity_id": "RNAC:URS00008B9C5E", "assessed_entity_type": "RNA", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": 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"name": "breast tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "mammary cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "primary breast cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "mammary tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "malignant neoplasm of breast", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" } ] }, "evidence_source": [ { "id": "27540977", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/27540977", "evidence_list": [ { "evidence": "The results revealed that the expression of H19 was significantly increased in BC tissues and plasma compared with healthy controls (P< 0.05)." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Circulating lncRNA H19 in plasma as a novel biomarker for breast cancer.", "journal": "Cancer biomarkers : section A of Disease markers", "authors": "Zhang K, Luo Z, Zhang Y, Zhang L, Wu L, Liu L, Yang J, Song X, Liu J", "date": "2016-08-20", "evidence": [], "reference": [ { "id": "27540977", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/27540977" } ] } ], "biomarker_canonical_id": "AN6629", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "f": "frequency", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6630-1", "biomarker_component": [ { "biomarker": "increased SREBP1 level", "assessed_biomarker_entity": 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In TCGA_PCa cohort study, high expression of SAMD5 was a risk factor for patients on post-operative BCR (HR 2.181, 95%CI 1.199‚Äì3.966, p=0.011) and this predictive ability was independent of Gleason score and pathologic T stage (HR 2.018, 95%CI 1.102‚Äì3.698, p=0.023). In another validating cohort study, the statistic trend was similar, and the pooled analysis by combining the two cohort study further confirmed its prognostic effect." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0002367" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, "synonyms": [ { "id": "DOID:10283", "name": "prostate neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "NGP - new growth of prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "tumor of the prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostate cancer, familial", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostatic neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "malignant tumor of the prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "hereditary prostate cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostatic cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" } ] }, "evidence_source": [ { "id": "30739268", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30739268", "evidence_list": [ { "evidence": "SAMD5 mRNA was shown to be up-regulated in multiple microarray datasets of prostate cancer with the strict statistic criteria: p<0.01 and fold change >/=2. In TCGA_PCa cohort study, high expression of SAMD5 was a risk factor for patients on post-operative BCR (HR 2.181, 95%CI 1.199‚Äì3.966, p=0.011) and this predictive ability was independent of Gleason score and pathologic T stage (HR 2.018, 95%CI 1.102‚Äì3.698, p=0.023). In another validating cohort study, the statistic trend was similar, and the pooled analysis by combining the two cohort study further confirmed its prognostic effect." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "SAMD5 mRNA was overexpressed in prostate cancer and can predict biochemical recurrence after radical prostatectomy.", "journal": "International urology and nephrology", "authors": "Li F, Xu Y, Liu RL", "date": "2019-02-11", "evidence": [], "reference": [ { "id": "30739268", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30739268" } ] } ], "biomarker_canonical_id": "AN6632", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "f": "frequency", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6633-1", "biomarker_component": [ { "biomarker": "increased HOXC6 level", "assessed_biomarker_entity": { "recommended_name": "Homeobox C6", "synonyms": [ { "synonym": "Homeobox protein CP25" }, { "synonym": "Homeobox protein HHO.C8" }, { "synonym": "Homeobox protein Hox-3C" } ] }, "assessed_biomarker_entity_id": "UPKB:P09630", "assessed_entity_type": "protein", "specimen": [ { "name": "prostate gland", "id": "UBERON:0002367", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0002367", "loinc_code": "" } ], "evidence_source": [ { "id": "31271305", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31271305", "evidence_list": [ { "evidence": "Relative expressions of HOXC6 at mRNA and protein levels were obviously higher in both PCa tissues and cells than in adjacent non-cancerous tissues and normal human prostate epithelial cells (p < .05). Chi-square test demonstrated that high expression of HOXC6 was significantly associated with PSA concentration, Gleason score and TNM stage (p < .05)." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0002367" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, "synonyms": [ { "id": "DOID:10283", "name": "prostate neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "NGP - new growth of prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "tumor of the prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostate cancer, familial", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostatic neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "malignant tumor of the prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "hereditary prostate cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostatic cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" } ] }, "evidence_source": [ { "id": "31271305", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31271305", "evidence_list": [ { "evidence": "Relative expressions of HOXC6 at mRNA and protein levels were obviously higher in both PCa tissues and cells than in adjacent non-cancerous tissues and normal human prostate epithelial cells (p < .05). Chi-square test demonstrated that high expression of HOXC6 was significantly associated with PSA concentration, Gleason score and TNM stage (p < .05)." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "", "journal": "Artificial cells, nanomedicine, and biotechnology", "authors": "Zhou J, Yang X, Song P, Wang H, Wang X", "date": "2019-07-05", "evidence": [], "reference": [ { "id": "31271305", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31271305" } ] } ], "biomarker_canonical_id": "AN6633", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6634-1", "biomarker_component": [ { "biomarker": "increased PNKD level", "assessed_biomarker_entity": { "recommended_name": "Myofibrillogenesis regulator 1", "synonyms": [ { "synonym": "BRP17" }, { "synonym": "DYT8" }, { "synonym": "FKSG19" }, { "synonym": "FPD1" }, { "synonym": "KIPP1184" }, { "synonym": "MR-1" }, { "synonym": "MR-1S" }, { "synonym": "MR1" }, { "synonym": "PDC" }, { "synonym": "PKND1" }, { "synonym": "PNKD1" }, { "synonym": "R1" }, { "synonym": "TAHCCP2" } ] }, "assessed_biomarker_entity_id": "NCBI: 25953", "assessed_entity_type": "gene", "specimen": [ { "name": "ovary", "id": "UBERON:0000992", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000992", "loinc_code": "" } ], "evidence_source": [ { "id": "21702971", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/21702971", "evidence_list": [ { "evidence": "MR-1 was overexpressed in ovarian cancer tissues and SKOV3 cells. Knockdown of MR-1 expression inhibited cell adhesion and invasion, and treatment with anti-cancer drugs decreased its expression in cancer cells. Taken together, these results provide the first evidence of the cellular and molecular mechanisms by which MR-1 might serve as a novel biological marker and potential therapeutic target for ovarian cancer." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000992" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:2394", "recommended_name": { "id": "DOID:2394", "name": "ovarian cancer", "description": "A female reproductive organ cancer that is located_in the ovary.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, "synonyms": [ { "id": "DOID:2394", "name": "primary ovarian cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "tumor of the Ovary", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "ovary neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "malignant tumour of ovary", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "malignant Ovarian tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "ovarian neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" } ] }, "evidence_source": [ { "id": "21702971", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/21702971", "evidence_list": [ { "evidence": "MR-1 was overexpressed in ovarian cancer tissues and SKOV3 cells. Knockdown of MR-1 expression inhibited cell adhesion and invasion, and treatment with anti-cancer drugs decreased its expression in cancer cells. Taken together, these results provide the first evidence of the cellular and molecular mechanisms by which MR-1 might serve as a novel biological marker and potential therapeutic target for ovarian cancer." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Myofibrillogenesis regulator 1 (MR-1) is a novel biomarker and potential therapeutic target for human ovarian cancer.", "journal": "BMC cancer", "authors": "Lu R, Sun M, Feng J, Gao X, Guo L", "date": "2011-06-28", "evidence": [], "reference": [ { "id": "21702971", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/21702971" } ] } ], "biomarker_canonical_id": "AN6634", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "c": "condition", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6635-1", "biomarker_component": [ { "biomarker": "increased AGR2 level", "assessed_biomarker_entity": { "recommended_name": "Anterior gradient protein 2 homolog", "synonyms": [ { "synonym": "AG-2" }, { "synonym": "hAG-2" }, { "synonym": "HPC8" }, { "synonym": "Secreted cement gland protein XAG-2 homolog" } ] }, "assessed_biomarker_entity_id": "UPKB:O95994", "assessed_entity_type": "protein", "specimen": [ { "name": "ovary", "id": "UBERON:0000992", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000992", "loinc_code": "" } ], "evidence_source": [ { "id": "21200134", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/21200134", "evidence_list": [ { "evidence": "We noted a marked overexpression of AGR2 mRNA and protein in early stage mucinous ovarian tumors compared to normal ovarian tissues and serous type ovarian tumors by Western blot analysis and immunohistochemistry. To further elucidate the role of AGR2 in ovarian tumorigenesis, stable 2774 human ovarian cancer cell lines overexpressing AGR2 were established. Forced expression of AGR2 in 2774 cells enhanced the growth and migration of ovarian cancer cells." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000992" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:2394", "recommended_name": { "id": "DOID:2394", "name": "ovarian cancer", "description": "A female reproductive organ cancer that is located_in the ovary.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, "synonyms": [ { "id": "DOID:2394", "name": "primary ovarian cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "tumor of the Ovary", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "ovary neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "malignant tumour of ovary", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "malignant Ovarian tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "ovarian neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" } ] }, "evidence_source": [ { "id": "21200134", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/21200134", "evidence_list": [ { "evidence": "We noted a marked overexpression of AGR2 mRNA and protein in early stage mucinous ovarian tumors compared to normal ovarian tissues and serous type ovarian tumors by Western blot analysis and immunohistochemistry. To further elucidate the role of AGR2 in ovarian tumorigenesis, stable 2774 human ovarian cancer cell lines overexpressing AGR2 were established. Forced expression of AGR2 in 2774 cells enhanced the growth and migration of ovarian cancer cells." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "AGR2, a mucinous ovarian cancer marker, promotes cell proliferation and migration.", "journal": "Experimental & molecular medicine", "authors": "Park K, Chung YJ, So H, Kim K, Park J, Oh M, Jo M, Choi K, Lee EJ, Choi YL, Song SY, Bae DS, Kim BG, Lee JH", "date": "2011-01-05", "evidence": [], "reference": [ { "id": "21200134", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/21200134" } ] } ], "biomarker_canonical_id": "AN6635", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6636-1", "biomarker_component": [ { "biomarker": "increased CTSD level", "assessed_biomarker_entity": { "recommended_name": "Cathepsin D", "synonyms": [] }, "assessed_biomarker_entity_id": "UPKB: P07339", "assessed_entity_type": "protein", "specimen": [ { "name": "stomach", "id": "UBERON:0000945", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000945", "loinc_code": "" } ], "evidence_source": [ { "id": "26998125", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/26998125", "evidence_list": [ { "evidence": "AGR2 and CTSD expression were both elevated in GC lesions compared with noncancerous tissues. In 204/436 (46.8%) GC patients, high expression of AGR2 was positively correlated with the expression of CTSD (r=0.577, P<0.01). Furthermore, several clinicopathological parameters were significantly associated with AGR2 expression level, including tumor size, depth of invasion and TNM stage (P<0.05). The findings of the present study indicate that AGR2 expression is significantly associated with location and size of GC, depth of invasion, TNM stage, lymphatic metastasis, vessel invasion, distant metastasis, Lauren's classification, high CTSD expression and poor prognosis. Thus, AGR2 may be a novel GC marker and may present a potential therapeutic target for GC." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000945" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" }, "synonyms": [ { "id": "DOID:10534", "name": "gastric neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" }, { "id": "DOID:10534", "name": "gastric cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" } ] }, "evidence_source": [ { "id": "26998125", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/26998125", "evidence_list": [ { "evidence": "AGR2 and CTSD expression were both elevated in GC lesions compared with noncancerous tissues. In 204/436 (46.8%) GC patients, high expression of AGR2 was positively correlated with the expression of CTSD (r=0.577, P<0.01). Furthermore, several clinicopathological parameters were significantly associated with AGR2 expression level, including tumor size, depth of invasion and TNM stage (P<0.05). The findings of the present study indicate that AGR2 expression is significantly associated with location and size of GC, depth of invasion, TNM stage, lymphatic metastasis, vessel invasion, distant metastasis, Lauren's classification, high CTSD expression and poor prognosis. Thus, AGR2 may be a novel GC marker and may present a potential therapeutic target for GC." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "AGR2 is associated with gastric cancer progression and poor survival.", "journal": "Oncology letters", "authors": "Zhang J, Jin Y, Xu S, Zheng J, Zhang QI, Wang Y, Chen J, Huang Y, He X, Zhao Z", "date": "2016-03-22", "evidence": [], "reference": [ { "id": "26998125", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/26998125" } ] } ], "biomarker_canonical_id": "AN6636", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "c": "condition", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6635-2", "biomarker_component": [ { "biomarker": "increased AGR2 level", "assessed_biomarker_entity": { "recommended_name": "Anterior gradient protein 2 homolog", "synonyms": [ { "synonym": "AG-2" }, { "synonym": "hAG-2" }, { "synonym": "HPC8" }, { "synonym": "Secreted cement gland protein XAG-2 homolog" } ] }, "assessed_biomarker_entity_id": "UPKB:O95994", "assessed_entity_type": "protein", "specimen": [ { "name": "stomach", "id": "UBERON:0000945", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000945", "loinc_code": "" } ], "evidence_source": [ { "id": "26998125", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/26998125", "evidence_list": [ { "evidence": "AGR2 and CTSD expression were both elevated in GC lesions compared with noncancerous tissues. In 204/436 (46.8%) GC patients, high expression of AGR2 was positively correlated with the expression of CTSD (r=0.577, P<0.01). Furthermore, several clinicopathological parameters were significantly associated with AGR2 expression level, including tumor size, depth of invasion and TNM stage (P<0.05). The findings of the present study indicate that AGR2 expression is significantly associated with location and size of GC, depth of invasion, TNM stage, lymphatic metastasis, vessel invasion, distant metastasis, Lauren's classification, high CTSD expression and poor prognosis. Thus, AGR2 may be a novel GC marker and may present a potential therapeutic target for GC." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000945" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" }, "synonyms": [ { "id": "DOID:10534", "name": "gastric neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" }, { "id": "DOID:10534", "name": "gastric cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" } ] }, "evidence_source": [ { "id": "26998125", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/26998125", "evidence_list": [ { "evidence": "AGR2 and CTSD expression were both elevated in GC lesions compared with noncancerous tissues. In 204/436 (46.8%) GC patients, high expression of AGR2 was positively correlated with the expression of CTSD (r=0.577, P<0.01). Furthermore, several clinicopathological parameters were significantly associated with AGR2 expression level, including tumor size, depth of invasion and TNM stage (P<0.05). The findings of the present study indicate that AGR2 expression is significantly associated with location and size of GC, depth of invasion, TNM stage, lymphatic metastasis, vessel invasion, distant metastasis, Lauren's classification, high CTSD expression and poor prognosis. Thus, AGR2 may be a novel GC marker and may present a potential therapeutic target for GC." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "AGR2 is associated with gastric cancer progression and poor survival.", "journal": "Oncology letters", "authors": "Zhang J, Jin Y, Xu S, Zheng J, Zhang QI, Wang Y, Chen J, Huang Y, He X, Zhao Z", "date": "2016-03-22", "evidence": [], "reference": [ { "id": "26998125", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/26998125" } ] } ], "biomarker_canonical_id": "AN6635", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "c": "condition", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6637-1", "biomarker_component": [ { "biomarker": "increased PLG level", "assessed_biomarker_entity": { "recommended_name": "Plasminogen", "synonyms": [] }, "assessed_biomarker_entity_id": "UPKB:P00747", "assessed_entity_type": "protein", "specimen": [ { "name": "ovary", "id": "UBERON:0000992", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000992", "loinc_code": "" } ], "evidence_source": [ { "id": "27935848", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/27935848", "evidence_list": [ { "evidence": "PLG staining was positively associated with prolonged overall survival (OS) [hazard ratio (HR)=0.59, p=0.026] of the patients. In summary, these data indicate that elevated PLG expression represents a favorable prognostic biomarker in advanced (FIGO III/IV) high-grade serous ovarian cancer." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000992" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:2394", "recommended_name": { "id": "DOID:2394", "name": "ovarian cancer", "description": "A female reproductive organ cancer that is located_in the ovary.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, "synonyms": [ { "id": "DOID:2394", "name": "primary ovarian cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "tumor of the Ovary", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "ovary neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "malignant tumour of ovary", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "malignant Ovarian tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "ovarian neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" } ] }, "evidence_source": [ { "id": "27935848", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/27935848", "evidence_list": [ { "evidence": "PLG staining was positively associated with prolonged overall survival (OS) [hazard ratio (HR)=0.59, p=0.026] of the patients. In summary, these data indicate that elevated PLG expression represents a favorable prognostic biomarker in advanced (FIGO III/IV) high-grade serous ovarian cancer." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Plasmin(ogen) serves as a favorable biomarker for prediction of survival in advanced high-grade serous ovarian cancer.", "journal": "Biological chemistry", "authors": "Zhao S, Dorn J, Napieralski R, Walch A, Diersch S, Kotzsch M, Ahmed N, Hooper JD, Kiechle M, Schmitt M, Magdolen V", "date": "2016-12-10", "evidence": [], "reference": [ { "id": "27935848", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/27935848" } ] } ], "biomarker_canonical_id": "AN6637", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 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CAP2 expression is upregulated in aggressive histologic types of epithelial ovarian cancer and serves as a novel prognostic biomarker for patient survival." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000992" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:2394", "recommended_name": { "id": "DOID:2394", "name": "ovarian cancer", "description": "A female reproductive organ cancer that is located_in the ovary.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, "synonyms": [ { "id": "DOID:2394", "name": "primary ovarian cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "tumor of the Ovary", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "ovary neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "malignant tumour of ovary", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "malignant Ovarian tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "ovarian neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" } ] }, "evidence_source": [ { "id": "32211793", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32211793", "evidence_list": [ { "evidence": "Multivariate analyses showed that CAP2 expression in ovarian cancer is an independent prognostic factor for recurrence-free survival (P = 0.019). CAP2 expression is upregulated in aggressive histologic types of epithelial ovarian cancer and serves as a novel prognostic biomarker for patient survival." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Upregulation of cyclase-associated actin cytoskeleton regulatory protein 2 in epithelial ovarian cancer correlates with aggressive histologic types and worse outcomes.", "journal": "Japanese journal of clinical oncology", "authors": "Adachi M, Masugi Y, Yamazaki K, Emoto K, Kobayashi Y, Tominaga E, Banno K, Aoki D, Sakamoto M", "date": "2020-03-27", "evidence": [], "reference": [ { "id": "32211793", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32211793" } ] } ], "biomarker_canonical_id": "AN6642", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "c": "condition", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6643-1", "biomarker_component": [ { "biomarker": "increased RNF126 level", "assessed_biomarker_entity": { "recommended_name": "RING finger protein 126", "synonyms": [ { "synonym": "RING finger protein 126" } ] }, "assessed_biomarker_entity_id": "UPKB:Q9BV68", "assessed_entity_type": "protein", "specimen": [ { "name": "ovary", "id": "UBERON:0000992", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000992", "loinc_code": "" } ], "evidence_source": [ { "id": "32254065", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32254065", "evidence_list": [ { "evidence": "Upregulated protein level of RNF126 in EOC tissues is a biomarker predicting poor outcomes of EOC patients." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000992" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:2394", "recommended_name": { "id": "DOID:2394", "name": "ovarian cancer", "description": "A female reproductive organ cancer that is located_in the ovary.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, "synonyms": [ { "id": "DOID:2394", "name": "primary ovarian cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "tumor of the Ovary", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "ovary neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "malignant tumour of ovary", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "malignant Ovarian tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "ovarian neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" } ] }, "evidence_source": [ { "id": "32254065", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32254065", "evidence_list": [ { "evidence": "Upregulated protein level of RNF126 in EOC tissues is a biomarker predicting poor outcomes of EOC patients." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "High Expression of RING Finger Protein 126 Predicts Unfavorable Prognosis of Epithelial Ovarian Cancer.", "journal": "Medical science monitor : international medical journal of experimental and clinical research", "authors": "Wang C, Wen A, Qiao J, Liu Y, Guo Y, Wang W", "date": "2020-04-08", "evidence": [], "reference": [ { "id": "32254065", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32254065" } ] } ], "biomarker_canonical_id": "AN6643", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6644-1", "biomarker_component": [ { "biomarker": "increased KLK10 level", "assessed_biomarker_entity": { "recommended_name": "Kallikrein-10", "synonyms": [ { "synonym": "Normal epithelial cell-specific 1" }, { "synonym": "Protease serine-like 1" } ] }, "assessed_biomarker_entity_id": "UPKB:O43240", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "12591730", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/12591730", "evidence_list": [ { "evidence": "HK10 concentration is significantly elevated in serum of presurgical ovarian cancer patients (range: 106-11,746 ng/liter; mean = 1067 ng/liter) but not in serum of patients with benign gynecologic diseases (range: 120-1200 ng/liter; mean = 447 ng/liter). Serum hK10 represents a novel biomarker for ovarian cancer. We conclude that preoperative serum hK10 concentration is a strong and independent unfavorable prognostic marker for ovarian cancer." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:2394", "recommended_name": { "id": "DOID:2394", "name": "ovarian cancer", "description": "A female reproductive organ cancer that is located_in the ovary.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, "synonyms": [ { "id": "DOID:2394", "name": "primary ovarian cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "tumor of the Ovary", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "ovary neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "malignant tumour of ovary", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "malignant Ovarian tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "ovarian neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" } ] }, "evidence_source": [ { "id": "12591730", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/12591730", "evidence_list": [ { "evidence": "HK10 concentration is significantly elevated in serum of presurgical ovarian cancer patients (range: 106-11,746 ng/liter; mean = 1067 ng/liter) but not in serum of patients with benign gynecologic diseases (range: 120-1200 ng/liter; mean = 447 ng/liter). Serum hK10 represents a novel biomarker for ovarian cancer. We conclude that preoperative serum hK10 concentration is a strong and independent unfavorable prognostic marker for ovarian cancer." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "The serum concentration of human kallikrein 10 represents a novel biomarker for ovarian cancer diagnosis and prognosis.", "journal": "Cancer research", "authors": "Luo LY, Katsaros D, Scorilas A, Fracchioli S, Bellino R, van Gramberen M, de Bruijn H, Henrik A, Stenman UH, Massobrio M, van der Zee AG, Vergote I, Diamandis EP", "date": "2003-02-20", "evidence": [], "reference": [ { "id": "12591730", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/12591730" } ] } ], "biomarker_canonical_id": "AN6644", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6645-1", "biomarker_component": [ { "biomarker": "increased STAT3 level", "assessed_biomarker_entity": { "recommended_name": "Signal transducer and activator of transcription 3", "synonyms": [ { "synonym": "Acute-phase response factor" } ] }, "assessed_biomarker_entity_id": "UPKB:P40763", "assessed_entity_type": "protein", "specimen": [ { "name": "thyroid gland", "id": "UBERON:0002046", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0002046", "loinc_code": "" } ], "evidence_source": [ { "id": "21577321", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/21577321", "evidence_list": [ { "evidence": "Expression of STAT3 in all PTC primary tumors was 98% (40/41) and thus significantly higher than corresponding benign thyroid tissue." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0002046" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:1781", "recommended_name": { "id": "DOID:1781", "name": "thyroid gland cancer", "description": "An endocrine gland cancer located in the thryoid gland located in the neck below the thyroid cartilage.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1781" }, "synonyms": [ { "id": "DOID:1781", "name": "neoplasm of thyroid gland", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1781" }, { "id": "DOID:1781", "name": "thyroid neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1781" }, { "id": "DOID:1781", "name": "thyroid gland cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1781" }, { "id": "DOID:1781", "name": "malignant tumour of thyroid gland", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1781" }, { "id": "DOID:1781", "name": "Thyroid gland neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1781" }, { "id": "DOID:1781", "name": "malignant neoplasm of thyroid gland", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1781" } ] }, "evidence_source": [ { "id": "21577321", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/21577321", "evidence_list": [ { "evidence": "Expression of STAT3 in all PTC primary tumors was 98% (40/41) and thus significantly higher than corresponding benign thyroid tissue." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Upregulation of the signal transducers and activators of transcription 3 (STAT3) pathway in lymphatic metastases of papillary thyroid cancer.", "journal": "International journal of clinical and experimental pathology", "authors": "Zhang J, Gill A, Atmore B, Johns A, Delbridge L, Lai R, McMullen T", "date": "2011-05-18", "evidence": [], "reference": [ { "id": "21577321", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/21577321" } ] } ], "biomarker_canonical_id": "AN6645", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "c": "condition", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6645-2", "biomarker_component": [ { "biomarker": "increased STAT3 level", "assessed_biomarker_entity": { "recommended_name": "Signal transducer and activator of transcription 3", "synonyms": [ { "synonym": "Acute-phase response factor" } ] }, "assessed_biomarker_entity_id": "UPKB:P40763", "assessed_entity_type": "protein", "specimen": [ { "name": "stomach", "id": "UBERON:0000945", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000945", "loinc_code": "" } ], "evidence_source": [ { "id": "26622669", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/26622669", "evidence_list": [ { "evidence": "The data demonstrated that eight genes associated with ApoE were differentially expressed, with six of these upregulated and two downregulated. Functionally, these genes were involved in the JAK-STAT cascade, acute-phase response, acute inflammatory response, and the steroid hormone response. Among these ApoE-associated genes, expression of the signal transducer and activator of transcription 2 (STAT2) and STAT3 transcription factors was upregulated. To the best of our knowledge, this is the first study to demonstrate the network of ApoE-related genes and transcription factors in gastric cancer. Additional studies are required in order to confirm these data and to translate the results into the identification of clinical biomarkers and novel treatment strategies for gastric cancer." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000945" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" }, "synonyms": [ { "id": "DOID:10534", "name": "gastric neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" }, { "id": "DOID:10534", "name": "gastric cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" } ] }, "evidence_source": [ { "id": "26622669", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/26622669", "evidence_list": [ { "evidence": "The data demonstrated that eight genes associated with ApoE were differentially expressed, with six of these upregulated and two downregulated. Functionally, these genes were involved in the JAK-STAT cascade, acute-phase response, acute inflammatory response, and the steroid hormone response. Among these ApoE-associated genes, expression of the signal transducer and activator of transcription 2 (STAT2) and STAT3 transcription factors was upregulated. To the best of our knowledge, this is the first study to demonstrate the network of ApoE-related genes and transcription factors in gastric cancer. Additional studies are required in order to confirm these data and to translate the results into the identification of clinical biomarkers and novel treatment strategies for gastric cancer." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Expression analysis of apolipoprotein E and its associated genes in gastric cancer.", "journal": "Oncology letters", "authors": "Shi X, Xu J, Wang J, Cui M, Gao Y, Niu H, Jin H", "date": "2015-12-02", "evidence": [], "reference": [ { "id": "26622669", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/26622669" } ] } ], "biomarker_canonical_id": "AN6645", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "w": "weight", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6646-1", "biomarker_component": [ { "biomarker": "increased SPHK1 level", "assessed_biomarker_entity": { "recommended_name": "Sphingosine kinase 1", "synonyms": [ { "synonym": "SK 1" }, { "synonym": "SPK 1" }, { "synonym": "Acetyltransferase SPHK1" } ] }, "assessed_biomarker_entity_id": "UPKB:Q9NYA1", "assessed_entity_type": "protein", "specimen": [ { "name": "thyroid gland", "id": "UBERON:0002046", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0002046", "loinc_code": "" } ], "evidence_source": [ { "id": "28982849", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/28982849", "evidence_list": [ { "evidence": "Sphingosine kinase 1 is up-regulated in many different types of human malignancies and plays a crucial role in cancer development and progression. Sphingosine kinase 1 expression in papillary thyroid carcinoma tissue was significantly higher than in nodular goiter (p<0.001) or normal thyroid (p<0.001) tissue." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0002046" } ] } ] } ], "best_biomarker_role": [ { "role": "predictive" } ], "condition": { "id": "DOID:1781", "recommended_name": { "id": "DOID:1781", "name": "thyroid gland cancer", "description": "An endocrine gland cancer located in the thryoid gland located in the neck below the thyroid cartilage.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1781" }, "synonyms": [ { "id": "DOID:1781", "name": "neoplasm of thyroid gland", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1781" }, { "id": "DOID:1781", "name": "thyroid neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1781" }, { "id": "DOID:1781", "name": "thyroid gland cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1781" }, { "id": "DOID:1781", "name": "malignant tumour of thyroid gland", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1781" }, { "id": "DOID:1781", "name": "Thyroid gland neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1781" }, { "id": "DOID:1781", "name": "malignant neoplasm of thyroid gland", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1781" } ] }, "evidence_source": [ { "id": "28982849", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/28982849", "evidence_list": [ { "evidence": "Sphingosine kinase 1 is up-regulated in many different types of human malignancies and plays a crucial role in cancer development and progression. Sphingosine kinase 1 expression in papillary thyroid carcinoma tissue was significantly higher than in nodular goiter (p<0.001) or normal thyroid (p<0.001) tissue." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Predictive Value of Sphingosine Kinase 1 Expression in Papillary Thyroid Carcinoma.", "journal": "Anticancer research", "authors": "Do SI, Kim HS, Kim K, Lee H, Do IG, Kim DH, Chae SW, Sohn JH", "date": "2017-10-07", "evidence": [], "reference": [ { "id": "28982849", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/28982849" } ] } ], "biomarker_canonical_id": "AN6646", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6647-1", "biomarker_component": [ { "biomarker": "increased PINX1 level", "assessed_biomarker_entity": { "recommended_name": "PIN2/TERF1 interacting telomerase inhibitor 1", "synonyms": [ { "synonym": "Liver-related putative tumor suppressor" }, { "synonym": "Pin2-interacting protein X1" }, { "synonym": "Protein 67-11-3" }, { "synonym": "TRF1-interacting protein 1" } ] }, "assessed_biomarker_entity_id": "UPKB:Q96BK5", "assessed_entity_type": "protein", "specimen": [ { "name": "thyroid gland", "id": "UBERON:0002046", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0002046", "loinc_code": "" } ], "evidence_source": [ { "id": "30026037", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30026037", "evidence_list": [ { "evidence": "Immunohistochemistry for PINX1 was performed using a tissue microarray of samples taken from the 160 patients with PTC. PINX1 expression was significantly associated with tumor size, lymph node metastasis, telomerase reverse transcriptase, promoter mutation and recurrence. PINX1 mRNA expression was more pronounced in the recurrent group than in the nonrecurrent group. In addition, results of the binary logistic regression model showed that PINX1 protein expression had a significant influence on recurrence." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0002046" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:1781", "recommended_name": { "id": "DOID:1781", "name": "thyroid gland cancer", "description": "An endocrine gland cancer located in the thryoid gland located in the neck below the thyroid cartilage.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1781" }, "synonyms": [ { "id": "DOID:1781", "name": "neoplasm of thyroid gland", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1781" }, { "id": "DOID:1781", "name": "thyroid neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1781" }, { "id": "DOID:1781", "name": "thyroid gland cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1781" }, { "id": "DOID:1781", "name": "malignant tumour of thyroid gland", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1781" }, { "id": "DOID:1781", "name": "Thyroid gland neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1781" }, { "id": "DOID:1781", "name": "malignant neoplasm of thyroid gland", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1781" } ] }, "evidence_source": [ { "id": "30026037", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30026037", "evidence_list": [ { "evidence": "Immunohistochemistry for PINX1 was performed using a tissue microarray of samples taken from the 160 patients with PTC. PINX1 expression was significantly associated with tumor size, lymph node metastasis, telomerase reverse transcriptase, promoter mutation and recurrence. PINX1 mRNA expression was more pronounced in the recurrent group than in the nonrecurrent group. In addition, results of the binary logistic regression model showed that PINX1 protein expression had a significant influence on recurrence." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "The clinical significance of PINX1 expression in papillary thyroid carcinoma.", "journal": "Human pathology", "authors": "Kang J, Han K, Kim HJ, Park JH, Kong JS, Park S, Myung JK", "date": "2018-07-22", "evidence": [], "reference": [ { "id": "30026037", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30026037" } ] } ], "biomarker_canonical_id": "AN6647", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "w": "weight", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6648-1", "biomarker_component": [ { "biomarker": "decreased PINX1 level", "assessed_biomarker_entity": { "recommended_name": "PIN2/TERF1 interacting telomerase inhibitor 1", "synonyms": [ { "synonym": "Liver-related putative tumor suppressor" }, { "synonym": "Pin2-interacting protein X1" }, { "synonym": "Protein 67-11-3" }, { "synonym": "TRF1-interacting protein 1" } ] }, "assessed_biomarker_entity_id": "UPKB:Q96BK5", "assessed_entity_type": "protein", "specimen": [ { "name": "kidney", "id": "UBERON:0002113", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0002113", "loinc_code": "" } ], "evidence_source": [ { "id": "26033551", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/26033551", "evidence_list": [ { "evidence": "PinX1 low expression staining was observed in 7 of 35 (20%) normal renal tissues, and 168 of 278 (60%) ccRCC tissues (P < 0.001) low PinX1 staining correlated with both worse overall and disease-specific survival in ccRCC (P = 0.002 and P = 0.002)." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0002113" } ] }, { "id": "31254127", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31254127", "evidence_list": [ { "evidence": "To further understand the molecular mechanism of PinX1 in renal cancer angiogenesis, we obtained the gene microarray to determine the downstream molecules of PinX1 in renal cancer. Surprisingly, PinX1 promoted the expression level of miR-125a-3p, which is a tumor suppressor of multiple oncogenes, including VEGF, CDK3, FUT5/6, and ERBB2/3." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0002113" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:263", "recommended_name": { "id": "DOID:263", "name": "kidney cancer", "description": "A urinary system cancer that is located_in the kidney.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_263" }, "synonyms": [ { "id": "DOID:263", "name": "malignant tumour of kidney", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_263" }, { "id": "DOID:263", "name": "malignant neoplasm of kidney except pelvis", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_263" }, { "id": "DOID:263", "name": "renal cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_263" } ] }, "evidence_source": [ { "id": "26033551", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/26033551", "evidence_list": [ { "evidence": "PinX1 low expression staining was observed in 7 of 35 (20%) normal renal tissues, and 168 of 278 (60%) ccRCC tissues (P < 0.001) low PinX1 staining correlated with both worse overall and disease-specific survival in ccRCC (P = 0.002 and P = 0.002)." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "31254127", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31254127", "evidence_list": [ { "evidence": "To further understand the molecular mechanism of PinX1 in renal cancer angiogenesis, we obtained the gene microarray to determine the downstream molecules of PinX1 in renal cancer. Surprisingly, PinX1 promoted the expression level of miR-125a-3p, which is a tumor suppressor of multiple oncogenes, including VEGF, CDK3, FUT5/6, and ERBB2/3." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "PinX1 serves as a potential prognostic indicator for clear cell renal cell carcinoma and inhibits its invasion and metastasis by suppressing MMP-2 via NF-κB-dependent transcription.", "journal": "Oncotarget", "authors": "Li HL, Han L, Chen HR, Meng F, Liu QH, Pan ZQ, Bai J, Zheng JN", "date": "2015-06-03", "evidence": [], "reference": [ { "id": "26033551", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/26033551" } ] }, { "title": "PinX1 represses renal cancer angiogenesis via the mir-125a-3p/VEGF signaling pathway.", "journal": "Angiogenesis", "authors": "Hou P, Li H, Yong H, Chen F, Chu S, Zheng J, Bai J", "date": "2019-06-30", "evidence": [], "reference": [ { "id": "31254127", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31254127" } ] } ], "biomarker_canonical_id": "AN6648", "score": 1.2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 1 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "c": "condition", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6649-1", "biomarker_component": [ { "biomarker": "decreased VEGF level", "assessed_biomarker_entity": { "recommended_name": "Vascular endothelial growth factor D", "synonyms": [ { "synonym": "VEGF-D" }, { "synonym": "c-Fos-induced growth factor" }, { "synonym": "FIGF" } ] }, "assessed_biomarker_entity_id": "UPKB:O43915", "assessed_entity_type": "protein", "specimen": [ { "name": "kidney", "id": "UBERON:0002113", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0002113", "loinc_code": "" } ], "evidence_source": [ { "id": "31254127", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31254127", "evidence_list": [ { "evidence": "To further understand the molecular mechanism of PinX1 in renal cancer angiogenesis, we obtained the gene microarray to determine the downstream molecules of PinX1 in renal cancer. 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Surprisingly, PinX1 promoted the expression level of miR-125a-3p, which is a tumor suppressor of multiple oncogenes, including VEGF, CDK3, FUT5/6, and ERBB2/3." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "PinX1 represses renal cancer angiogenesis via the mir-125a-3p/VEGF signaling pathway.", "journal": "Angiogenesis", "authors": "Hou P, Li H, Yong H, Chen F, Chu S, Zheng J, Bai J", "date": "2019-06-30", "evidence": [], "reference": [ { "id": "31254127", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31254127" } ] } ], "biomarker_canonical_id": "AN6649", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "c": "condition", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6650-1", "biomarker_component": [ { "biomarker": "increased miR-125a-3p", "assessed_biomarker_entity": { "recommended_name": "microRNA-125a-3p", "synonyms": [] }, "assessed_biomarker_entity_id": "MRB:MI0000469", "assessed_entity_type": "RNA", "specimen": [ { "name": "kidney", "id": "UBERON:0002113", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0002113", "loinc_code": "" } ], "evidence_source": [ { "id": "31254127", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31254127", "evidence_list": [ { "evidence": "To further understand the molecular mechanism of PinX1 in renal cancer angiogenesis, we obtained the gene microarray to determine the downstream molecules of PinX1 in renal cancer. 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Oncology", "authors": "Moore LE, Pfeiffer RM, Poscablo C, Real FX, Kogevinas M, Silverman D, García-Closas R, Chanock S, Tardón A, Serra C, Carrato A, Dosemeci M, García-Closas M, Esteller M, Fraga M, Rothman N, Malats N", "date": "2008-03-15", "evidence": [], "reference": [ { "id": "18339581", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/18339581" } ] } ], "biomarker_canonical_id": "AN6651", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "c": "condition", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6652-1", "biomarker_component": [ { "biomarker": "increased DKK-1 level", "assessed_biomarker_entity": { "recommended_name": "Dickkopf-1", "synonyms": [ { "synonym": "Dickkopf-1" }, { "synonym": "Dkk-1" }, { "synonym": "hDkk-1" }, { "synonym": "SK" } ] }, "assessed_biomarker_entity_id": "UPKB:O94907", "assessed_entity_type": "protein", "specimen": [ { "name": "prostate gland", "id": "UBERON:0002367", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0002367", "loinc_code": "" } ], "evidence_source": [ { "id": "18561248", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/18561248", "evidence_list": [ { "evidence": "DKK-1 expression index (EI) was found to increase in PIN and primary lesions compared to non-neoplastic tissue (106¬±10 vs. 19¬±6, respectively, where the EI is the product of the percent expression and staining intensity). DKK-1 expression was also found to be higher in all PCa metastatic lesions (56¬±21 EI) compared to non-neoplastic tissues but was significantly decreased vs. primary PCa lesions (p<0.008). The decline in DKK-1 correlated with a shift of beta-catenin staining from the nucleus to the cytoplasm suggesting possible mechanism for the observed decrease in DKK-1 levels during PCa progression. Within metastatic lesions, DKK-1 expression was least abundant in PCa bone metastases relative to all soft tissue PCa metastatic lesions except lymph node metastases. High DKK-1 expression within PCa metastases was further associated with shorter over-all patient survival." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0002367" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, "synonyms": [ { "id": "DOID:10283", "name": "prostate neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "NGP - new growth of prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "tumor of the prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostate cancer, familial", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostatic neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "malignant tumor of the prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "hereditary prostate cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostatic cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" } ] }, "evidence_source": [ { "id": "18561248", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/18561248", "evidence_list": [ { "evidence": "DKK-1 expression index (EI) was found to increase in PIN and primary lesions compared to non-neoplastic tissue (106¬±10 vs. 19¬±6, respectively, where the EI is the product of the percent expression and staining intensity). DKK-1 expression was also found to be higher in all PCa metastatic lesions (56¬±21 EI) compared to non-neoplastic tissues but was significantly decreased vs. primary PCa lesions (p<0.008). The decline in DKK-1 correlated with a shift of beta-catenin staining from the nucleus to the cytoplasm suggesting possible mechanism for the observed decrease in DKK-1 levels during PCa progression. Within metastatic lesions, DKK-1 expression was least abundant in PCa bone metastases relative to all soft tissue PCa metastatic lesions except lymph node metastases. High DKK-1 expression within PCa metastases was further associated with shorter over-all patient survival." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Dickkopf-1 expression increases early in prostate cancer development and decreases during progression from primary tumor to metastasis.", "journal": "The Prostate", "authors": "Hall CL, Daignault SD, Shah RB, Pienta KJ, Keller ET", "date": "2008-06-19", "evidence": [], "reference": [ { "id": "18561248", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/18561248" } ] } ], "biomarker_canonical_id": "AN6652", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "f": "frequency", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6653-1", "biomarker_component": [ { "biomarker": "increased DPP-4 level", "assessed_biomarker_entity": { "recommended_name": "Dipeptidyl peptidase-IV", "synonyms": [ { "synonym": "ADABP" }, { "synonym": "Adenosine deaminase complexing protein 2" }, { "synonym": "ADCP-2" }, { "synonym": "Dipeptidyl peptidase IV" }, { "synonym": "DPP IV" }, { "synonym": "T-cell activation antigen CD26" }, { "synonym": "TP103" } ] }, "assessed_biomarker_entity_id": "UPKB:P27487", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "30594915", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30594915", "evidence_list": [ { "evidence": "The serum DPP-IV concentration was measured in 171 male patients with PTC, 81 male patients with a benign thyroid nodule (BTN), and 52 male healthy controls (HCs). he ROC curve indicated a good performance of DPP-IV for discriminating PTC from BTN, with an area under the curve (AUC) of 0.881 (95% CI, 0.840-0.922). Serum DPP-IV demonstrated a modest performance in predicting nonstructurally persistent disease/recurrent disease (NSPRD) survival." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "predictive" } ], "condition": { "id": "DOID:1781", "recommended_name": { "id": "DOID:1781", "name": "thyroid gland cancer", "description": "An endocrine gland cancer located in the thryoid gland located in the neck below the thyroid cartilage.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1781" }, "synonyms": [ { "id": "DOID:1781", "name": "neoplasm of thyroid gland", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1781" }, { "id": "DOID:1781", "name": "thyroid neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1781" }, { "id": "DOID:1781", "name": "thyroid gland cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1781" }, { "id": "DOID:1781", "name": "malignant tumour of thyroid gland", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1781" }, { "id": "DOID:1781", "name": "Thyroid gland neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1781" }, { "id": "DOID:1781", "name": "malignant neoplasm of thyroid gland", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1781" } ] }, "evidence_source": [ { "id": "30594915", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30594915", "evidence_list": [ { "evidence": "The serum DPP-IV concentration was measured in 171 male patients with PTC, 81 male patients with a benign thyroid nodule (BTN), and 52 male healthy controls (HCs). he ROC curve indicated a good performance of DPP-IV for discriminating PTC from BTN, with an area under the curve (AUC) of 0.881 (95% CI, 0.840-0.922). Serum DPP-IV demonstrated a modest performance in predicting nonstructurally persistent disease/recurrent disease (NSPRD) survival." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Predictive significance of serum dipeptidyl peptidase-IV in papillary thyroid carcinoma.", "journal": "Cancer biomarkers : section A of Disease markers", "authors": "Zhang N, Cong X, Zhou D, Guo L, Yuan C, Xu D, Su C", "date": "2018-12-31", "evidence": [], "reference": [ { "id": "30594915", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30594915" } ] } ], "biomarker_canonical_id": "AN6653", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "f": "frequency", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6654-1", "biomarker_component": [ { "biomarker": "increased CHL1 level", "assessed_biomarker_entity": { "recommended_name": "Close homolog of L1", "synonyms": [ { "synonym": "Close homolog of L1" } ] }, "assessed_biomarker_entity_id": "UPKB:O00533", "assessed_entity_type": "protein", "specimen": [ { "name": "thyroid gland", "id": "UBERON:0002046", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0002046", "loinc_code": "" } ], "evidence_source": [ { "id": "30311656", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30311656", "evidence_list": [ { "evidence": "CHL1 was found to have greater than 15-fold higher expression in fragments per kilobase million in HCC compared with benign Hurthle cell tumors. This was confirmed by qRT-PCR. Moreover, the immunoreactivity score of the CHL1 protein was significantly higher in HCC compared with benign H√ºrthle cell nodules. Moreover, the immunoreactivity score of the CHL1 protein was significantly higher in HCC compared with benign H√ºrthle cell nodules. CHL1 expression may represent a novel and useful prognostic biomarker to distinguish HCC from benign H√ºrthle cell disease." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0002046" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:1781", "recommended_name": { "id": "DOID:1781", "name": "thyroid gland cancer", "description": "An endocrine gland cancer located in the thryoid gland located in the neck below the thyroid cartilage.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1781" }, "synonyms": [ { "id": "DOID:1781", "name": "neoplasm of thyroid gland", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1781" }, { "id": "DOID:1781", "name": "thyroid neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1781" }, { "id": "DOID:1781", "name": "thyroid gland cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1781" }, { "id": "DOID:1781", "name": "malignant tumour of thyroid gland", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1781" }, { "id": "DOID:1781", "name": "Thyroid gland neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1781" }, { "id": "DOID:1781", "name": "malignant neoplasm of thyroid gland", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1781" } ] }, "evidence_source": [ { "id": "30311656", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30311656", "evidence_list": [ { "evidence": "CHL1 was found to have greater than 15-fold higher expression in fragments per kilobase million in HCC compared with benign Hurthle cell tumors. This was confirmed by qRT-PCR. Moreover, the immunoreactivity score of the CHL1 protein was significantly higher in HCC compared with benign H√ºrthle cell nodules. Moreover, the immunoreactivity score of the CHL1 protein was significantly higher in HCC compared with benign H√ºrthle cell nodules. CHL1 expression may represent a novel and useful prognostic biomarker to distinguish HCC from benign H√ºrthle cell disease." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "CHL1 expression differentiates Hürthle cell carcinoma from benign Hürthle cell nodules.", "journal": "Journal of surgical oncology", "authors": "Li W, Xia S, Aronova A, Min IM, Verma A, Scognamiglio T, Gray KD, Ullmann TM, Liang H, Moore MD, Elemento O, Zarnegar R, Fahey TJ", "date": "2018-10-13", "evidence": [], "reference": [ { "id": "30311656", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30311656" } ] } ], "biomarker_canonical_id": "AN6654", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "f": "frequency", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6655-1", "biomarker_component": [ { "biomarker": "increased NPM level", "assessed_biomarker_entity": { "recommended_name": "Nucleophosmin", "synonyms": [ { "synonym": "NPM" }, { "synonym": "Nucleolar phosphoprotein B23" }, { "synonym": "Nucleolar protein NO38" }, { "synonym": "Numatrin" } ] }, "assessed_biomarker_entity_id": "UPKB:P06748", "assessed_entity_type": "protein", "specimen": [ { "name": "thyroid gland", "id": "UBERON:0002046", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0002046", "loinc_code": "" } ], "evidence_source": [ { "id": "20515654", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/20515654", "evidence_list": [ { "evidence": "In these cells, a positive correlation between NPM protein levels, but not mRNA, and proliferation state was detected. By using thyroid tumor cell lines, we demonstrated that such a post-mRNA regulation may depend on NPM binding to p-Akt, whose levels were found to be increased in the tumor cells, in parallel with reduction of PTEN. In conclusion, our present data demonstrate for the first time that nucleophosmin is overexpressed in thyroid tumors, as an early event of thyroid tumorigenesis." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0002046" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:1781", "recommended_name": { "id": "DOID:1781", "name": "thyroid gland cancer", "description": "An endocrine gland cancer located in the thryoid gland located in the neck below the thyroid cartilage.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1781" }, "synonyms": [ { "id": "DOID:1781", "name": "neoplasm of thyroid gland", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1781" }, { "id": "DOID:1781", "name": "thyroid neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1781" }, { "id": "DOID:1781", "name": "thyroid gland cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1781" }, { "id": "DOID:1781", "name": "malignant tumour of thyroid gland", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1781" }, { "id": "DOID:1781", "name": "Thyroid gland neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1781" }, { "id": "DOID:1781", "name": "malignant neoplasm of thyroid gland", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1781" } ] }, "evidence_source": [ { "id": "20515654", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/20515654", "evidence_list": [ { "evidence": "In these cells, a positive correlation between NPM protein levels, but not mRNA, and proliferation state was detected. By using thyroid tumor cell lines, we demonstrated that such a post-mRNA regulation may depend on NPM binding to p-Akt, whose levels were found to be increased in the tumor cells, in parallel with reduction of PTEN. In conclusion, our present data demonstrate for the first time that nucleophosmin is overexpressed in thyroid tumors, as an early event of thyroid tumorigenesis." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Nucleophosmin is overexpressed in thyroid tumors.", "journal": "Biochemical and biophysical research communications", "authors": "Pianta A, Puppin C, Franzoni A, Fabbro D, Di Loreto C, Bulotta S, Deganuto M, Paron I, Tell G, Puxeddu E, Filetti S, Russo D, Damante G", "date": "2010-06-03", "evidence": [], "reference": [ { "id": "20515654", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/20515654" } ] } ], "biomarker_canonical_id": "AN6655", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "f": "frequency", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6656-1", "biomarker_component": [ { "biomarker": "ACTG1 amplification", "assessed_biomarker_entity": { "recommended_name": "Actin gamma 1 gene", "synonyms": [ { "synonym": "ACT" }, { "synonym": "ACTG" }, { "synonym": "DFNA20" }, { "synonym": "DFNA26" }, { "synonym": "HEL-176" } ] }, "assessed_biomarker_entity_id": "NCBI: 71", "assessed_entity_type": "gene", "specimen": [ { "name": "uterus", "id": "UBERON:0000995", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000995", "loinc_code": "" } ], "evidence_source": [ { "id": "33217970", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/33217970", "evidence_list": [ { "evidence": "Given that ACTG1 and MYLK2 amplifications or overexpression were consistently observed in uterine cancers, we sought to analyze their potential as uterine cancer biomarkers. We found that patients with ACTG1 gains in the UCEC cohort, relative to those without, had a worse prognosis, while patients with MYLK2 gains did not. Based on Kaplan-Meier curves, ACTG1 gains predicted significantly shorter overall survival (p-value = 6.198 √ó 10-4)." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000995" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:363", "recommended_name": { "id": "DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, "synonyms": [ { "id": "DOID:363", "name": "uterine tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "neoplasm of uterus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "Tumour of uterus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "malignant uterine tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "malignant neoplasm of uterus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "CA - cancer of uterus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "uterus neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" } ] }, "evidence_source": [ { "id": "33217970", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/33217970", "evidence_list": [ { "evidence": "Given that ACTG1 and MYLK2 amplifications or overexpression were consistently observed in uterine cancers, we sought to analyze their potential as uterine cancer biomarkers. We found that patients with ACTG1 gains in the UCEC cohort, relative to those without, had a worse prognosis, while patients with MYLK2 gains did not. Based on Kaplan-Meier curves, ACTG1 gains predicted significantly shorter overall survival (p-value = 6.198 √ó 10-4)." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Genomic Amplification and Functional Dependency of the Gamma Actin Gene ", "journal": "International journal of molecular sciences", "authors": "Richter C, Mayhew D, Rennhack JP, So J, Stover EH, Hwang JH, Szczesna-Cordary D", "date": "2020-11-22", "evidence": [], "reference": [ { "id": "33217970", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/33217970" } ] } ], "biomarker_canonical_id": "AN6656", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "w": "weight", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6778-1", "biomarker_component": [ { "biomarker": "Increased HINT1 level", "assessed_biomarker_entity": { "recommended_name": "Histidine Triad Nucleotide-Binding Protein 1", "synonyms": [] }, "assessed_biomarker_entity_id": "UPKB:HINT1", "assessed_entity_type": "protein", "specimen": [ { "name": "prostate gland", "id": "UBERON:0002367", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0002367", "loinc_code": "" } ], "evidence_source": [ { "id": "24386364", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/24386364", "evidence_list": [ { "evidence": "Increase in the expression of BTF3, HINT1, NDRG1 and ODC1 in malignant cores, diagnosed by histopathology, compared to non-malignant cores (p<0.0001, Mann Whitney U test). These results identify BTF3, HINT1, NDRG1 and ODC1 as proteins that are overexpressed in prostate cancer. NDRG1 could be a useful protein biomarker for prostate cancer." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0002367" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, "synonyms": [ { "id": "DOID:10283", "name": "prostate neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "NGP - new growth of prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "tumor of the prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostate cancer, familial", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostatic neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "malignant tumor of the prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "hereditary prostate cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostatic cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" } ] }, "evidence_source": [ { "id": "24386364", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/24386364", "evidence_list": [ { "evidence": "Increase in the expression of BTF3, HINT1, NDRG1 and ODC1 in malignant cores, diagnosed by histopathology, compared to non-malignant cores (p<0.0001, Mann Whitney U test). These results identify BTF3, HINT1, NDRG1 and ODC1 as proteins that are overexpressed in prostate cancer. 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High amounts of p185 were significantly associated with a high expression of urokinase-type plasminogen activator (uPA) (P <.010), uPA-receptor (P =.030), type-1 plasminogen activator inhibitor (PAI) (P <.010), type-2 PAI (P =.021), cathepsin D (P =.036), matrix metalloproteinase-2 (P =. 024), alpha-1-antichymotrypsin (P =.025), and alpha-2-macroglobulin (P =.017). Multivariate analysis considering these proteases/protease inhibitors, in addition to alpha-1-antitrypsin, tissue plasminogen activator, plasminogen, alpha-2-antiplasmin, and antithrombin III, and established prognostic parameters revealed that, in addition to surgical curability, pT stage, pN stage, and PAI-1, c-erbB-2 is an independent prognostic factor for overall survival of curatively resected patients (n = 139; P =.049; relative risk, 1.54; 95% confidence interval, 1.08 to 1.67) and all patients (P =.028; relative risk 1.33; 95% CI, 1.28 to 1.38)." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "c-erbB-2 is of independent prognostic relevance in gastric cancer and is associated with the expression of tumor-associated protease systems.", "journal": "Journal of clinical oncology : official journal of the American Society of Clinical Oncology", "authors": "Allgayer H, Babic R, Gruetzner KU, Tarabichi A, Schildberg FW, Heiss MM", "date": "2000-06-01", "evidence": [], "reference": [ { "id": "10829039", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/10829039" } ] } ], "biomarker_canonical_id": "AN6661", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "c": "condition", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6662-1", "biomarker_component": [ { "biomarker": "increased RCAS1 level", "assessed_biomarker_entity": { "recommended_name": "Receptor-binding cancer antigen expressed on SiSo cells", "synonyms": [ { "synonym": "Cancer-associated surface antigen RCAS1" }, { "synonym": "Estrogen receptor-binding fragment-associated gene 9 protein" } ] }, "assessed_biomarker_entity_id": "UPKB:O00559", "assessed_entity_type": "protein", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "16842844", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/16842844", "evidence_list": [ { "evidence": "Uterine cancer patients had significantly higher serum RCAS1 concentrations than did healthy women. The RCAS1 level was dramatically reduced in patients who had a positive response to treatment; however, the RCAS1 value increased in patients whose tumors clearly grew (P= 0.0007 and P= 0.0008, respectively) (Fig. 3)." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "predictive" } ], "condition": { "id": "DOID:363", "recommended_name": { "id": "DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, "synonyms": [ { "id": "DOID:363", "name": "uterine tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "neoplasm of uterus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "Tumour of uterus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "malignant uterine tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "malignant neoplasm of uterus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "CA - cancer of uterus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "uterus neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" } ] }, "evidence_source": [ { "id": "16842844", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/16842844", "evidence_list": [ { "evidence": "Uterine cancer patients had significantly higher serum RCAS1 concentrations than did healthy women. The RCAS1 level was dramatically reduced in patients who had a positive response to treatment; however, the RCAS1 value increased in patients whose tumors clearly grew (P= 0.0007 and P= 0.0008, respectively) (Fig. 3)." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Clinical significance of RCAS1 as a biomarker of uterine cancer.", "journal": "Gynecologic oncology", "authors": "Sonoda K, Miyamoto S, Hirakawa T, Yagi H, Yotsumoto F, Nakashima M, Watanabe T, Nakano H", "date": "2006-07-18", "evidence": [], "reference": [ { "id": "16842844", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/16842844" } ] } ], "biomarker_canonical_id": "AN6662", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, 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"evidence": "Amplification of the FGFR2 gene was identified in a subset of Chinese and Caucasian patients with gastric cancer." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "FGFR2 gene amplification in gastric cancer predicts sensitivity to the selective FGFR inhibitor AZD4547.", "journal": "Clinical cancer research : an official journal of the American Association for Cancer Research", "authors": "Xie L, Su X, Zhang L, Yin X, Tang L, Zhang X, Xu Y, Gao Z, Liu K, Zhou M, Gao B, Shen D, Zhang L, Ji J, Gavine PR, Zhang J, Kilgour E, Zhang X, Ji Q", "date": "2013-03-16", "evidence": [], "reference": [ { "id": "23493349", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/23493349" } ] } ], "biomarker_canonical_id": "AN5140", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, 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assessable patients, MET CNG five or more copies and homozygous HGF-truncated DATE occurred in 21 patients (10%) and 30 patients (13%), respectively. Patients with MET CNG five or more copies (MET-positive) showed significantly worse prognosis with multivariate hazard ratio (HR) of 3.02 (95% CI, 1.71 to 5.33; P < .001) for DFS and multivariate HR of 2.91 (95% CI, 1.65 to 5.11; P < .001) for OS." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000945" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" }, "synonyms": [ { "id": "DOID:10534", "name": "gastric neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" }, { "id": "DOID:10534", "name": "gastric cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" } ] }, "evidence_source": [ { "id": "22042954", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/22042954", "evidence_list": [ { "evidence": "In 216 assessable patients, MET CNG five or more copies and homozygous HGF-truncated DATE occurred in 21 patients (10%) and 30 patients (13%), respectively. Patients with MET CNG five or more copies (MET-positive) showed significantly worse prognosis with multivariate hazard ratio (HR) of 3.02 (95% CI, 1.71 to 5.33; P < .001) for DFS and multivariate HR of 2.91 (95% CI, 1.65 to 5.11; P < .001) for OS." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Genetic activation of the MET pathway and prognosis of patients with high-risk, radically resected gastric cancer.", "journal": "Journal of clinical oncology : official journal of the American Society of Clinical Oncology", "authors": "Graziano F, Galluccio N, Lorenzini P, Ruzzo A, Canestrari E, D'Emidio S, Catalano V, Sisti V, Ligorio C, Andreoni F, Rulli E, Di Oto E, Fiorentini G, Zingaretti C, De Nictolis M, Cappuzzo F, Magnani M", "date": "2011-11-02", "evidence": [], "reference": [ { "id": "22042954", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/22042954" } ] } ], "biomarker_canonical_id": "AN6663", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "c": "condition", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6664-1", "biomarker_component": [ { "biomarker": "PIK3CA gene amplification", "assessed_biomarker_entity": { "recommended_name": "Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform gene", "synonyms": [ { "synonym": "CCM4" }, { "synonym": "CLAPO" }, { "synonym": "CLOVE" }, { "synonym": "CWS5" }, { "synonym": "HMH" }, { "synonym": "MCAP" }, { "synonym": "MCM" }, { "synonym": "MCMTC" }, { "synonym": "PI3K" }, { "synonym": "PI3K-alpha" }, { "synonym": "p110-alpha" } ] }, "assessed_biomarker_entity_id": "NCBI: 5290", "assessed_entity_type": "gene", "specimen": [ { "name": "stomach", "id": "UBERON:0000945", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000945", "loinc_code": "63419-6" } ], "evidence_source": [ { "id": "22292935", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/22292935", "evidence_list": [ { "evidence": "PIK3CA mutations and amplification were found in 8/113 (7.1%) and 88/131 (67%) gastric cancer patients, respectively. Our data showed that PIK3CA mutations were not common, but its amplification was very common in gastric cancer and may be a major mechanism in activating the PI3K/Akt pathway in gastric cancer. Importantly, Kaplan-Meier survival curves revealed that PIK3CA amplification was significantly positively associated with poor survival of gastric cancer patients. In the present study, a high prevalence of PIK3CA amplification was found in gastric cancer, which was significantly associated with poor prognosis of gastric cancer patients." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000945" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" }, "synonyms": [ { "id": "DOID:10534", "name": "gastric neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" }, { "id": "DOID:10534", "name": "gastric cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" } ] }, "evidence_source": [ { "id": "22292935", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/22292935", "evidence_list": [ { "evidence": "PIK3CA mutations and amplification were found in 8/113 (7.1%) and 88/131 (67%) gastric cancer patients, respectively. Our data showed that PIK3CA mutations were not common, but its amplification was very common in gastric cancer and may be a major mechanism in activating the PI3K/Akt pathway in gastric cancer. Importantly, Kaplan-Meier survival curves revealed that PIK3CA amplification was significantly positively associated with poor survival of gastric cancer patients. In the present study, a high prevalence of PIK3CA amplification was found in gastric cancer, which was significantly associated with poor prognosis of gastric cancer patients." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Highly frequent PIK3CA amplification is associated with poor prognosis in gastric cancer.", "journal": "BMC cancer", "authors": "Shi J, Yao D, Liu W, Wang N, Lv H, Zhang G, Ji M, Xu L, He N, Shi B, Hou P", "date": "2012-02-02", "evidence": [], "reference": [ { "id": "22292935", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/22292935" } ] } ], "biomarker_canonical_id": "AN6664", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "f": "frequency", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6665-1", "biomarker_component": [ { "biomarker": "decreased P2RX7 level", "assessed_biomarker_entity": { "recommended_name": "P2X purinoceptor 7", "synonyms": [ { "synonym": "P2X7" }, { "synonym": "ATP receptor" }, { "synonym": "P2Z receptor" }, { "synonym": "Purinergic receptor" } ] }, "assessed_biomarker_entity_id": "UPKB:Q99572", "assessed_entity_type": "protein", "specimen": [ { "name": "uterus", "id": "UBERON:0000995", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000995", "loinc_code": "" } ], "evidence_source": [ { "id": "17035398", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/17035398", "evidence_list": [ { "evidence": "The P2X7 is expressed predominantly in the epithelial components of the uterus, (a) Levels of the P2X(7) are lower in uterine epithelial cancer tissues than in the corresponding normal tissues. (b) The data suggest that tissue P2X(7) mRNA and protein levels could be used as a novel biomarker to differentiate normal and cancer uterine epithelial tissues. Uterine epithelial cancerous lesions lack expression of the P2X7." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000995" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:363", "recommended_name": { "id": "DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, "synonyms": [ { "id": "DOID:363", "name": "uterine tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "neoplasm of uterus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "Tumour of uterus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "malignant uterine tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "malignant neoplasm of uterus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "CA - cancer of uterus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "uterus neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" } ] }, "evidence_source": [ { "id": "17035398", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/17035398", "evidence_list": [ { "evidence": "The P2X7 is expressed predominantly in the epithelial components of the uterus, (a) Levels of the P2X(7) are lower in uterine epithelial cancer tissues than in the corresponding normal tissues. (b) The data suggest that tissue P2X(7) mRNA and protein levels could be used as a novel biomarker to differentiate normal and cancer uterine epithelial tissues. Uterine epithelial cancerous lesions lack expression of the P2X7." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "The P2X7 receptor: a novel biomarker of uterine epithelial cancers.", "journal": "Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology", "authors": "Li X, Zhou L, Feng YH, Abdul-Karim FW, Gorodeski GI", "date": "2006-10-13", "evidence": [], "reference": [ { "id": "17035398", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/17035398" } ] } ], "biomarker_canonical_id": "AN6665", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", 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0.003), and endometrioid carcinoma patients (P = 0.005)." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "monitoring" } ], "condition": { "id": "DOID:363", "recommended_name": { "id": "DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, "synonyms": [ { "id": "DOID:363", "name": "uterine tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "neoplasm of uterus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "Tumour of uterus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "malignant uterine tumor", "resource": "Disease Ontology", 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Higher pre-treatment GGT serum levels were independently associated with unfavorable prognosis in women with ULMS. Thus, GGT seems to be a useful novel biomarker in ULMS." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:363", "recommended_name": { "id": "DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, "synonyms": [ { "id": "DOID:363", "name": "uterine tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "neoplasm of uterus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "Tumour of uterus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "malignant uterine tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "malignant neoplasm of uterus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "CA - cancer of uterus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "uterus neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" } ] }, "evidence_source": [ { "id": "27646551", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/27646551", "evidence_list": [ { "evidence": "Women with higher pre-treatment GGT serum levels showed impaired Overall Survival (OS) compared to women with normal low levels. Higher pre-treatment GGT serum levels were independently associated with unfavorable prognosis in women with ULMS. Thus, GGT seems to be a useful novel biomarker in ULMS." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Gamma-glutamyltransferase as novel biomarker in patients with uterine leiomyosarcoma.", "journal": "Scientific reports", "authors": "Schwameis R, Grimm C, Brodowicz T, Petru E, Hefler-Frischmuth K, Staudigl C, Reinthaller A, Heinze G, Polterauer S, Polterauer M", "date": "2016-09-21", "evidence": [], "reference": [ { "id": "27646551", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/27646551" } ] } ], "biomarker_canonical_id": "AN6383", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "w": "weight", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6671-1", "biomarker_component": [ { "biomarker": "decreased PSMB9 level", "assessed_biomarker_entity": { "recommended_name": "Proteasome subunit beta type 9", "synonyms": [ { "synonym": "Low molecular mass protein 2" }, { "synonym": "Macropain chain 7" }, { "synonym": "Multicatalytic endopeptidase complex chain 7" }, { "synonym": "Proteasome chain 7" }, { "synonym": "Proteasome subunit beta-1i" }, { "synonym": "Really interesting new gene 12 protein" } ] }, "assessed_biomarker_entity_id": "UPKB:P28065", "assessed_entity_type": "protein", "specimen": [ { "name": "uterus", "id": "UBERON:0000995", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000995", "loinc_code": "" } ], "evidence_source": [ { "id": "28482675", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/28482675", "evidence_list": [ { "evidence": "The immunohistochemistry (IHC) experiments, performed separately at several medical facilities, revealed a serious loss in the ability to induce PSMB9/beta1i expression in human uterine LMS tissues in comparison with normal human myometrium tissues located in same tissue sections." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000995" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:363", "recommended_name": { "id": "DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, "synonyms": [ { "id": "DOID:363", "name": "uterine tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "neoplasm of uterus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "Tumour of uterus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "malignant uterine tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "malignant neoplasm of uterus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "CA - cancer of uterus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "uterus neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" } ] }, "evidence_source": [ { "id": "28482675", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/28482675", "evidence_list": [ { "evidence": "The immunohistochemistry (IHC) experiments, performed separately at several medical facilities, revealed a serious loss in the ability to induce PSMB9/beta1i expression in human uterine LMS tissues in comparison with normal human myometrium tissues located in same tissue sections." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "A novel diagnostic biomarker for human uterine leiomyosarcoma: PSMB9/β1i.", "journal": "Chinese clinical oncology", "authors": "Hayashi T, Kawano M, Sano K, Ichimura T, Gur G, Yaish P, Zharhary D, Kanai Y, Tonegawa S, Shiozawa T, Yaegashi N, Konishi I", "date": "2017-05-10", "evidence": [], "reference": [ { "id": "28482675", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/28482675" } ] } ], "biomarker_canonical_id": "AN6671", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "f": "frequency", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6672-1", "biomarker_component": [ { "biomarker": "increased ACKR3 level", "assessed_biomarker_entity": { "recommended_name": "Atypical chemokine receptor 3", "synonyms": [ { "synonym": "C-X-C chemokine receptor type 7" }, { "synonym": "CXC-R7" }, { "synonym": "CXCR-7" }, { "synonym": "Chemokine orphan receptor 1" }, { "synonym": "G-protein coupled receptor 159" }, { "synonym": "G-protein coupled receptor RDC1 homolog" }, { "synonym": "RDC-1" } ] }, "assessed_biomarker_entity_id": "UPKB:P25106", "assessed_entity_type": "protein", "specimen": [ { "name": "esophagus", "id": "UBERON:0001043", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0001043", "loinc_code": "" } ], "evidence_source": [ { "id": "33709176", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/33709176", "evidence_list": [ { "evidence": "High CXCR7 expression was associated with poor prognosis in patients with EAC, and high expression of CXCR7 with its ligand CXCL12 had a stronger association with prognosis. High CXCR7 expression was significantly associated with lymphatic invasion (present vs absent, P = 0.005) and higher number of lymph node metastases (pN0-1 vs pN2-3, P = 0.0014)." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0001043" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, "synonyms": [ { "id": "DOID:5041", "name": "Ca lower third oesophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant tumor of abdominal esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "Ca middle third oesophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant neoplasm of upper third esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "esophagus cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" } ] }, "evidence_source": [ { "id": "33709176", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/33709176", "evidence_list": [ { "evidence": "High CXCR7 expression was associated with poor prognosis in patients with EAC, and high expression of CXCR7 with its ligand CXCL12 had a stronger association with prognosis. High CXCR7 expression was significantly associated with lymphatic invasion (present vs absent, P = 0.005) and higher number of lymph node metastases (pN0-1 vs pN2-3, P = 0.0014)." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Prognostic Impact of CXCR7 and CXCL12 Expression in Patients with Esophageal Adenocarcinoma.", "journal": "Annals of surgical oncology", "authors": "Goto M, Shibahara Y, Baciu C, Allison F, Yeung JC, Darling GE, Liu M", "date": "2021-03-13", "evidence": [], "reference": [ { "id": "33709176", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/33709176" } ] } ], "biomarker_canonical_id": "AN6672", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6595-2", "biomarker_component": [ { "biomarker": "increased CXCR4 level", "assessed_biomarker_entity": { "recommended_name": "C-X-C chemokine receptor type 4", "synonyms": [ { "synonym": "CXC-R4" }, { "synonym": "CXCR-4" }, { "synonym": "FB22" }, { "synonym": "Fusin" }, { "synonym": "HM89" }, { "synonym": "LCR1" }, { "synonym": "Leukocyte-derived seven transmembrane domain receptor" }, { "synonym": "LESTR" }, { "synonym": "Lipopolysaccharide-associated protein 3" }, { "synonym": "LAP-3" }, { "synonym": "LPS-associated protein 3" }, { "synonym": "NPYRL" }, { "synonym": "Stromal cell-derived factor 1 receptor" }, { "synonym": "SDF-1 receptor" } ] }, "assessed_biomarker_entity_id": "UPKB:P61073", "assessed_entity_type": "protein", "specimen": [ { "name": "esophagus", "id": "UBERON:0001043", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0001043", "loinc_code": "" } ], "evidence_source": [ { "id": "27439769", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/27439769", "evidence_list": [ { "evidence": "Immunohistochemistry revealed positive CXCR4 and CXCL12 expression in 48 (61 %) and 62 (78 %) patients, respectively. The MIB-1 proliferation index was markedly higher in ESCC with a positive expression of CXCR4 or CXCL12." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0001043" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, "synonyms": [ { "id": "DOID:5041", "name": "Ca lower third oesophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant tumor of abdominal esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "Ca middle third oesophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant neoplasm of upper third esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "esophagus cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" } ] }, "evidence_source": [ { "id": "27439769", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/27439769", "evidence_list": [ { "evidence": "Immunohistochemistry revealed positive CXCR4 and CXCL12 expression in 48 (61 %) and 62 (78 %) patients, respectively. The MIB-1 proliferation index was markedly higher in ESCC with a positive expression of CXCR4 or CXCL12." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "CXCL12 expression promotes esophageal squamous cell carcinoma proliferation and worsens the prognosis.", "journal": "BMC cancer", "authors": "Uchi Y, Takeuchi H, Matsuda S, Saikawa Y, Kawakubo H, Wada N, Takahashi T, Nakamura R, Fukuda K, Omori T, Kitagawa Y", "date": "2016-07-22", "evidence": [], "reference": [ { "id": "27439769", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/27439769" } ] } ], "biomarker_canonical_id": "AN6595", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "c": "condition", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6673-1", "biomarker_component": [ { "biomarker": "increased CXCR12 level", "assessed_biomarker_entity": { "recommended_name": "Stromal cell-derived factor 1", "synonyms": [ { "synonym": "SDF-1" }, { "synonym": "hSDF-1" }, { "synonym": "C-X-C motif chemokine 12" }, { "synonym": "Intercrine reduced in hepatomas" }, { "synonym": "IRH" }, { "synonym": "hIRH" }, { "synonym": "Pre-B cell growth-stimulating factor" }, { "synonym": "PBSF" } ] }, "assessed_biomarker_entity_id": "UPKB:P48061", "assessed_entity_type": "protein", "specimen": [ { "name": "esophagus", "id": "UBERON:0001043", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0001043", "loinc_code": "" } ], "evidence_source": [ { "id": "27439769", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/27439769", "evidence_list": [ { "evidence": "Immunohistochemistry revealed positive CXCR4 and CXCL12 expression in 48 (61 %) and 62 (78 %) patients, respectively. The MIB-1 proliferation index was markedly higher in ESCC with a positive expression of CXCR4 or CXCL12." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0001043" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, "synonyms": [ { "id": "DOID:5041", "name": "Ca lower third oesophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant tumor of abdominal esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "Ca middle third oesophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant neoplasm of upper third esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" }, { "id": "DOID:5041", "name": "esophagus cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_5041" } ] }, "evidence_source": [ { "id": "27439769", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/27439769", "evidence_list": [ { "evidence": "Immunohistochemistry revealed positive CXCR4 and CXCL12 expression in 48 (61 %) and 62 (78 %) patients, respectively. The MIB-1 proliferation index was markedly higher in ESCC with a positive expression of CXCR4 or CXCL12." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "CXCL12 expression promotes esophageal squamous cell carcinoma proliferation and worsens the prognosis.", "journal": "BMC cancer", "authors": "Uchi Y, Takeuchi H, Matsuda S, Saikawa Y, Kawakubo H, Wada N, Takahashi T, Nakamura R, Fukuda K, Omori T, Kitagawa Y", "date": "2016-07-22", "evidence": [], "reference": [ { "id": "27439769", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/27439769" } ] } ], "biomarker_canonical_id": "AN6673", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "f": "frequency", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6674-1", "biomarker_component": [ { "biomarker": "decreased GKN1 level", "assessed_biomarker_entity": { "recommended_name": "Gastrokine 1", "synonyms": [ { "synonym": "AMP18" }, { "synonym": "BRICD1" }, { "synonym": "CA11" }, { "synonym": "FOV" }, { "synonym": "foveolin" } ] }, "assessed_biomarker_entity_id": "NCBI: 56287", "assessed_entity_type": "gene", "specimen": [ { "name": "stomach", "id": "UBERON:0000945", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000945", "loinc_code": "" } ], "evidence_source": [ { "id": "25469040", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/25469040", "evidence_list": [ { "evidence": "The present study investigated GNK1 expression in different mucosa biopsy specimens from gastric cancer, cancer-adjacent lesions, atrophic gastritis and normal control subjects (superficial gastritis patients). We found that GKN1 mRNA expression was progressively downregulated from corresponding distant non-tumour tissues to tumour tissues, and was lower than in the control tissues of both groups. This suggested that low or absent expression of GKN1 may contribute to gastric carcinogenesis. This is consistent with a previous study that demonstrated decreased GKN1 expression in gastric cancer tissues. In addition, we analysed GKN1 expression in two types of gastric cancer and found that the mRNA level of GKN1 was lower in patients with diffuse type gastric cancer. This indicates that GKN1 may be related to tumour classification." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000945" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" }, "synonyms": [ { "id": "DOID:10534", "name": "gastric neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" }, { "id": "DOID:10534", "name": "gastric cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" } ] }, "evidence_source": [ { "id": "25469040", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/25469040", "evidence_list": [ { "evidence": "The present study investigated GNK1 expression in different mucosa biopsy specimens from gastric cancer, cancer-adjacent lesions, atrophic gastritis and normal control subjects (superficial gastritis patients). We found that GKN1 mRNA expression was progressively downregulated from corresponding distant non-tumour tissues to tumour tissues, and was lower than in the control tissues of both groups. This suggested that low or absent expression of GKN1 may contribute to gastric carcinogenesis. This is consistent with a previous study that demonstrated decreased GKN1 expression in gastric cancer tissues. In addition, we analysed GKN1 expression in two types of gastric cancer and found that the mRNA level of GKN1 was lower in patients with diffuse type gastric cancer. This indicates that GKN1 may be related to tumour classification." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Decreased expression of gastrokine 1 in gastric mucosa of gastric cancer patients.", "journal": "World journal of gastroenterology", "authors": "Guo XY, Dong L, Qin B, Jiang J, Shi AM", "date": "2014-12-04", "evidence": [], "reference": [ { "id": "25469040", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/25469040" } ] } ], "biomarker_canonical_id": "AN6674", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6675-1", "biomarker_component": [ { "biomarker": "increased methylation in RORA", "assessed_biomarker_entity": { "recommended_name": "Nuclear receptor ROR-alpha gene promoter methylation", "synonyms": [ { "synonym": "IDDECA" }, { "synonym": "NR1F1" }, { "synonym": "ROR1" }, { "synonym": "ROR2" }, { "synonym": "ROR3" }, { "synonym": "RORa1" }, { "synonym": "RORalpha" }, { "synonym": "RZR-ALPHA" }, { "synonym": "RZRA" } ] }, "assessed_biomarker_entity_id": "NCBI: 6095", "assessed_entity_type": "gene", "specimen": [ { "name": "stomach", "id": "UBERON:0000945", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000945", "loinc_code": "" } ], "evidence_source": [ { "id": "19375421", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/19375421", "evidence_list": [ { "evidence": "When considering progressive stages, 2 patterns were evident: (1) type 1 markers, showing consistently high levels of methylation in both gastric dysplasia and cancer (MINT25 and GDNF); (2) type 2 markers, showing high levels of methylation in early gastric cancer and gastric dysplasia but decreased levels in advanced gastric cancer (RORA, ADAM23, PRDM5, and MLF1). Of interest, use of the type 2 markers showed higher methylation levels in gastric dysplasia than in advanced gastric cancer (P < .001), which is consistent with our studies in ulcerative colitis and colon cancer. RORA and MINT25 were more hypermethylated in intestinal type GCs than those of diffuse type GCs, whereas CDH1 showed opposite patterns of methylation." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000945" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" }, "synonyms": [ { "id": "DOID:10534", "name": "gastric neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" }, { "id": "DOID:10534", "name": "gastric cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" } ] }, "evidence_source": [ { "id": "19375421", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/19375421", "evidence_list": [ { "evidence": "When considering progressive stages, 2 patterns were evident: (1) type 1 markers, showing consistently high levels of methylation in both gastric dysplasia and cancer (MINT25 and GDNF); (2) type 2 markers, showing high levels of methylation in early gastric cancer and gastric dysplasia but decreased levels in advanced gastric cancer (RORA, ADAM23, PRDM5, and MLF1). Of interest, use of the type 2 markers showed higher methylation levels in gastric dysplasia than in advanced gastric cancer (P < .001), which is consistent with our studies in ulcerative colitis and colon cancer. RORA and MINT25 were more hypermethylated in intestinal type GCs than those of diffuse type GCs, whereas CDH1 showed opposite patterns of methylation." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Sensitive and specific detection of early gastric cancer with DNA methylation analysis of gastric washes.", "journal": "Gastroenterology", "authors": "Watanabe Y, Kim HS, Castoro RJ, Chung W, Estecio MR, Kondo K, Guo Y, Ahmed SS, Toyota M, Itoh F, Suk KT, Cho MY, Shen L, Jelinek J, Issa JP", "date": "2009-04-21", "evidence": [], "reference": [ { "id": "19375421", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/19375421" } ] } ], "biomarker_canonical_id": "AN6675", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "f": "frequency", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6676-1", "biomarker_component": [ { "biomarker": "increased COX-2 level", "assessed_biomarker_entity": { "recommended_name": "Cyclooxygenase-2", "synonyms": [ { "synonym": "Cyclooxygenase-2" }, { "synonym": "COX-2" }, { "synonym": "PHS II" }, { "synonym": "Prostaglandin H2 synthase 2" }, { "synonym": "PGH synthase 2" }, { "synonym": "PGHS-2" }, { "synonym": "Prostaglandin-endoperoxide synthase 2" } ] }, "assessed_biomarker_entity_id": "UPKB:P35354", "assessed_entity_type": "protein", "specimen": [ { "name": "uterus", "id": "UBERON:0000995", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000995", "loinc_code": "49476-5" } ], "evidence_source": [ { "id": "15589595", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/15589595", "evidence_list": [ { "evidence": "COX-2 overexpression was noted in one third of the cases in both early and advanced stage disease. These patients fared significantly worse than those without COX-2 overexpression." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000995" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:363", "recommended_name": { "id": "DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, "synonyms": [ { "id": "DOID:363", "name": "uterine tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "neoplasm of uterus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "Tumour of uterus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "malignant uterine tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "malignant neoplasm of uterus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "CA - cancer of uterus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "uterus neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" } ] }, "evidence_source": [ { "id": "15589595", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/15589595", "evidence_list": [ { "evidence": "COX-2 overexpression was noted in one third of the cases in both early and advanced stage disease. These patients fared significantly worse than those without COX-2 overexpression." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "COX-2, c-KIT and HER-2/neu expression in uterine carcinosarcomas: prognostic factors or potential markers for targeted therapies?", "journal": "Gynecologic oncology", "authors": "Raspollini MR, Susini T, Amunni G, Paglierani M, Taddei A, Marchionni M, Scarselli G, Taddei GL", "date": "2004-12-14", "evidence": [], "reference": [ { "id": "15589595", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/15589595" } ] } ], "biomarker_canonical_id": "AN6676", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "c": "condition", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6781-1", "biomarker_component": [ { "biomarker": "increased FABP3 level", "assessed_biomarker_entity": { "recommended_name": "Fatty acid binding protein-3", "synonyms": [ { "synonym": "Fatty acid-binding protein 3" }, { "synonym": "Heart-type fatty acid-binding protein" }, { "synonym": "H-FABP" }, { "synonym": "Mammary-derived growth inhibitor" }, { "synonym": "MDGI" }, { "synonym": "Muscle fatty acid-binding protein" }, { "synonym": "M-FABP" } ] }, "assessed_biomarker_entity_id": "UPKB:P05413", "assessed_entity_type": "protein", "specimen": [ { "name": "uterus", "id": "UBERON:0000995", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000995", "loinc_code": "" } ], "evidence_source": [ { "id": "28643014", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/28643014", "evidence_list": [ { "evidence": "The presence of any degree of NAV2, assessed in 159 of these patients who had informative cores, was significantly related to shorter Overall Survival (OS) (p = 0.037; Fig. 2a). Expression was analyzed for association with clinicopathologic parameters and survival. TGLN (p < 0.001), NAV2 (p < 0.001), and FABP3 (p = 0.005) were overexpressed in LMS compared to LG-ESS, whereas nuclear CCND2 (p < 0.001) was overexpressed in LG-ESS. NAV2 and CCND2 are novel candidate prognostic markers in LMS and LG-ESS, respectively." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000995" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:363", "recommended_name": { "id": "DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, "synonyms": [ { "id": "DOID:363", "name": "uterine tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "neoplasm of uterus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "Tumour of uterus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "malignant uterine tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "malignant neoplasm of uterus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "CA - cancer of uterus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "uterus neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" } ] }, "evidence_source": [ { "id": "28643014", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/28643014", "evidence_list": [ { "evidence": "The presence of any degree of NAV2, assessed in 159 of these patients who had informative cores, was significantly related to shorter Overall Survival (OS) (p = 0.037; Fig. 2a). Expression was analyzed for association with clinicopathologic parameters and survival. TGLN (p < 0.001), NAV2 (p < 0.001), and FABP3 (p = 0.005) were overexpressed in LMS compared to LG-ESS, whereas nuclear CCND2 (p < 0.001) was overexpressed in LG-ESS. NAV2 and CCND2 are novel candidate prognostic markers in LMS and LG-ESS, respectively." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Neuron navigator-2 and cyclin D2 are new candidate prognostic markers in uterine sarcoma.", "journal": "Virchows Archiv : an international journal of pathology", "authors": "Davidson B, Hellesylt E, Holth A, Danielsen HE, Skeie-Jensen T, Katz B", "date": "2017-06-24", "evidence": [], "reference": [ { "id": "28643014", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/28643014" } ] } ], "biomarker_canonical_id": "AN6781", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6678-1", "biomarker_component": [ { "biomarker": "increased NAV2 level", "assessed_biomarker_entity": { "recommended_name": "Neuron navigator-2", "synonyms": [ { "synonym": "Helicase APC down-regulated 1" }, { "synonym": "Pore membrane and/or filament-interacting-like protein 2" }, { "synonym": "Retinoic acid inducible in neuroblastoma 1" }, { "synonym": "Steerin-2" }, { "synonym": "Unc-53 homolog 2" }, { "synonym": "unc53H2" } ] }, "assessed_biomarker_entity_id": "UPKB:Q8IVL1", "assessed_entity_type": "protein", "specimen": [ { "name": "uterus", "id": "UBERON:0000995", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000995", "loinc_code": "" } ], "evidence_source": [ { "id": "28643014", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/28643014", "evidence_list": [ { "evidence": "The presence of any degree of NAV2, assessed in 159 of these patients who had informative cores, was significantly related to shorter Overall Survival (OS) (p = 0.037; Fig. 2a). Expression was analyzed for association with clinicopathologic parameters and survival. TGLN (p < 0.001), NAV2 (p < 0.001), and FABP3 (p = 0.005) were overexpressed in LMS compared to LG-ESS, whereas nuclear CCND2 (p < 0.001) was overexpressed in LG-ESS. NAV2 and CCND2 are novel candidate prognostic markers in LMS and LG-ESS, respectively." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000995" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:363", "recommended_name": { "id": "DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, "synonyms": [ { "id": "DOID:363", "name": "uterine tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "neoplasm of uterus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "Tumour of uterus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "malignant uterine tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "malignant neoplasm of uterus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "CA - cancer of uterus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "uterus neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" } ] }, "evidence_source": [ { "id": "28643014", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/28643014", "evidence_list": [ { "evidence": "The presence of any degree of NAV2, assessed in 159 of these patients who had informative cores, was significantly related to shorter Overall Survival (OS) (p = 0.037; Fig. 2a). Expression was analyzed for association with clinicopathologic parameters and survival. TGLN (p < 0.001), NAV2 (p < 0.001), and FABP3 (p = 0.005) were overexpressed in LMS compared to LG-ESS, whereas nuclear CCND2 (p < 0.001) was overexpressed in LG-ESS. NAV2 and CCND2 are novel candidate prognostic markers in LMS and LG-ESS, respectively." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Neuron navigator-2 and cyclin D2 are new candidate prognostic markers in uterine sarcoma.", "journal": "Virchows Archiv : an international journal of pathology", "authors": "Davidson B, Hellesylt E, Holth A, Danielsen HE, Skeie-Jensen T, Katz B", "date": "2017-06-24", "evidence": [], "reference": [ { "id": "28643014", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/28643014" } ] } ], "biomarker_canonical_id": "AN6678", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6679-1", "biomarker_component": [ { "biomarker": "increased CCND2 level", "assessed_biomarker_entity": { "recommended_name": "Cyclin D2", "synonyms": [] }, "assessed_biomarker_entity_id": "UPKB:P30279", "assessed_entity_type": "protein", "specimen": [ { "name": "uterus", "id": "UBERON:0000995", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000995", "loinc_code": "" } ], "evidence_source": [ { "id": "28643014", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/28643014", "evidence_list": [ { "evidence": "The presence of nuclear CCND2 expression in >10% tumor cells, assessed in 62 of these patients who had informative cores, was significantly related to longer Overall Survival (OS) (p = 0.012; Fig. 2b). TGLN (p < 0.001), NAV2 (p < 0.001), and FABP3 (p = 0.005) were overexpressed in LMS compared to LG ESS, whereas nuclear CCND2 (p < 0.001) was overexpressed in LG-ESS. NAV2 expression was associated with shorter overall survival in patients with LMS (p = 0.037), whereas nuclear CCND2 expression in LG-ESS was significantly related to longer survival (p = 0.012) in univariate analysis. Nuclear CCND2 expression was an independent prognosticator in Cox multivariate analysis (p = 0.023). In conclusion, TGLN, FABP3, NAV2, and nuclear CCND2 aid in differentiating LG-ESS from LMS. NAV2 and CCND2 are novel candidate prognostic markers in LMS and LG-ESS, respectively." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000995" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:363", "recommended_name": { "id": "DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, "synonyms": [ { "id": "DOID:363", "name": "uterine tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "neoplasm of uterus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "Tumour of uterus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "malignant uterine tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "malignant neoplasm of uterus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "CA - cancer of uterus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "uterus neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" } ] }, "evidence_source": [ { "id": "28643014", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/28643014", "evidence_list": [ { "evidence": "The presence of nuclear CCND2 expression in >10% tumor cells, assessed in 62 of these patients who had informative cores, was significantly related to longer Overall Survival (OS) (p = 0.012; Fig. 2b). TGLN (p < 0.001), NAV2 (p < 0.001), and FABP3 (p = 0.005) were overexpressed in LMS compared to LG ESS, whereas nuclear CCND2 (p < 0.001) was overexpressed in LG-ESS. NAV2 expression was associated with shorter overall survival in patients with LMS (p = 0.037), whereas nuclear CCND2 expression in LG-ESS was significantly related to longer survival (p = 0.012) in univariate analysis. Nuclear CCND2 expression was an independent prognosticator in Cox multivariate analysis (p = 0.023). In conclusion, TGLN, FABP3, NAV2, and nuclear CCND2 aid in differentiating LG-ESS from LMS. NAV2 and CCND2 are novel candidate prognostic markers in LMS and LG-ESS, respectively." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Neuron navigator-2 and cyclin D2 are new candidate prognostic markers in uterine sarcoma.", "journal": "Virchows Archiv : an international journal of pathology", "authors": "Davidson B, Hellesylt E, Holth A, Danielsen HE, Skeie-Jensen T, Katz B", "date": "2017-06-24", "evidence": [], "reference": [ { "id": "28643014", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/28643014" } ] } ], "biomarker_canonical_id": "AN6679", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6680-1", "biomarker_component": [ { "biomarker": "increased TAGLN level", "assessed_biomarker_entity": { "recommended_name": "Transgelin", "synonyms": [ { "synonym": "22 kDa actin-binding protein" }, { "synonym": "Protein WS3-10" }, { "synonym": "Smooth muscle protein 22-alpha" }, { "synonym": "SM22-alpha" } ] }, "assessed_biomarker_entity_id": "UPKB:Q01995", "assessed_entity_type": "protein", "specimen": [ { "name": "smooth muscle tissue", "id": "UBERON:0001135", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0001135", "loinc_code": "" } ], "evidence_source": [ { "id": "23174934", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/23174934", "evidence_list": [ { "evidence": "For the diagnosis of leiomyosarcomas versus all other sarcomas including GIST, transgelin emerged as the best diagnostic marker with 83% Se, 82% Sp, a PPV of 67%, a NPV of 92% and an accuracy rate of 83%." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0001135" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:363", "recommended_name": { "id": "DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, "synonyms": [ { "id": "DOID:363", "name": "uterine tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "neoplasm of uterus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "Tumour of uterus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "malignant uterine tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "malignant neoplasm of uterus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "CA - cancer of uterus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "uterus neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" } ] }, "evidence_source": [ { "id": "23174934", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/23174934", "evidence_list": [ { "evidence": "For the diagnosis of leiomyosarcomas versus all other sarcomas including GIST, transgelin emerged as the best diagnostic marker with 83% Se, 82% Sp, a PPV of 67%, a NPV of 92% and an accuracy rate of 83%." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Transgelin is a novel marker of smooth muscle differentiation that improves diagnostic accuracy of leiomyosarcomas: a comparative immunohistochemical reappraisal of myogenic markers in 900 soft tissue tumors.", "journal": "Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc", "authors": "Robin YM, Penel N, Pérot G, Neuville A, Vélasco V, Ranchère-Vince D, Terrier P, Coindre JM", "date": "2012-11-24", "evidence": [], "reference": [ { "id": "23174934", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/23174934" } ] } ], "biomarker_canonical_id": "AN6680", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "c": "condition", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6681-1", "biomarker_component": [ { "biomarker": "increased IMP3 level", "assessed_biomarker_entity": { "recommended_name": "Insulin-like growth factor II messenger RNA-binding protein-3", "synonyms": [ { "synonym": "U3 snoRNP protein IMP3" }, { "synonym": "BRMS2" } ] }, "assessed_biomarker_entity_id": "UPKB:Q9NV31", "assessed_entity_type": "protein", "specimen": [ { "name": "uterus", "id": "UBERON:0000995", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000995", "loinc_code": "" } ], "evidence_source": [ { "id": "18223334", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/18223334", "evidence_list": [ { "evidence": "IMP3 expression was predominantly found in endometrial serous carcinoma and its putative precursor lesions, with 3 (14%) of 21 endometrial glandular dysplasia, 16 (89%) of 18 serous endometrial intraepithelial carcinoma, and 48 (94%) of 51 serous carcinomas (P<0.001). We conclude that expression of IMP3, a newly identified cytoplasmic marker, is closely associated with type II endometrial cancer. It seems that IMP3 expression is associated with an aggressive histologic phenotype among endometrial neoplastic lesions. Strong and diffuse IMP3 expression is highly sensitive for endometrial serous and clear cell carcinomas including their putative precursor lesions. Therefore, IMP3 may be a useful diagnostic marker in the assessment of endometrial cancers and their precursor lesions, particularly when the amount of available tissue material is limited and a concern of type II cancer arises." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000995" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:363", "recommended_name": { "id": "DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, "synonyms": [ { "id": "DOID:363", "name": "uterine tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "neoplasm of uterus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "Tumour of uterus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "malignant uterine tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "malignant neoplasm of uterus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "CA - cancer of uterus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "uterus neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" } ] }, "evidence_source": [ { "id": "18223334", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/18223334", "evidence_list": [ { "evidence": "IMP3 expression was predominantly found in endometrial serous carcinoma and its putative precursor lesions, with 3 (14%) of 21 endometrial glandular dysplasia, 16 (89%) of 18 serous endometrial intraepithelial carcinoma, and 48 (94%) of 51 serous carcinomas (P<0.001). We conclude that expression of IMP3, a newly identified cytoplasmic marker, is closely associated with type II endometrial cancer. It seems that IMP3 expression is associated with an aggressive histologic phenotype among endometrial neoplastic lesions. Strong and diffuse IMP3 expression is highly sensitive for endometrial serous and clear cell carcinomas including their putative precursor lesions. Therefore, IMP3 may be a useful diagnostic marker in the assessment of endometrial cancers and their precursor lesions, particularly when the amount of available tissue material is limited and a concern of type II cancer arises." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "The oncofetal protein IMP3: a novel biomarker for endometrial serous carcinoma.", "journal": "The American journal of surgical pathology", "authors": "Zheng W, Yi X, Fadare O, Liang SX, Martel M, Schwartz PE, Jiang Z", "date": "2008-01-29", "evidence": [], "reference": [ { "id": "18223334", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/18223334" } ] } ], "biomarker_canonical_id": "AN6681", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "c": "condition", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6682-1", "biomarker_component": [ { "biomarker": "increased CD10 level", "assessed_biomarker_entity": { "recommended_name": "Cluster of differentiation 10", "synonyms": [ { "synonym": "Atriopeptidase" }, { "synonym": "Common acute lymphocytic leukemia antigen" }, { "synonym": "CALLA" }, { "synonym": "Enkephalinase" }, { "synonym": "Neutral endopeptidase 24.11" }, { "synonym": "NEP" }, { "synonym": "Neutral endopeptidase" }, { "synonym": "Skin fibroblast elastase" }, { "synonym": "SFE" } ] }, "assessed_biomarker_entity_id": "UPKB:P08473", "assessed_entity_type": "protein", "specimen": [ { "name": "uterus", "id": "UBERON:0000995", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000995", "loinc_code": "51214-5" } ], "evidence_source": [ { "id": "15571618", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/15571618", "evidence_list": [ { "evidence": "Uterine Adenosarcoma (UAS) with sarcomatous overgrowth stained strongly positive in five of eight (63%) cases. Pattern of strong positivity was focal in four of five (80%). These findings suggest that CD10 can be used to differentiate UAS from cellular leiomyoma, or in case endometrial stromal cells exhibit muscle differentiation. Furthermore, CD10 positivity in recurrent UAS might guide the pathologist toward an endometrial stromal origin." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000995" } ] }, { "id": "11532038", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/11532038", "evidence_list": [ { "evidence": "CD10 is a reliable and sensitive immunohistochemical marker of normal endometrial stroma. Positivity, which is often strong and/or diffuse is found in endometrial stromal nodules and low-grade ESS. Positive staining with CD10, when strong and diffuse, may be useful in distinguishing these tumours from histological mimics, especially cellular leiomyoma and AGCT which are generally negative. There was positive staining of all low-grade Endometrial stromal sarcoma (ESS)." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000995" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:363", "recommended_name": { "id": "DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, "synonyms": [ { "id": "DOID:363", "name": "uterine tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "neoplasm of uterus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "Tumour of uterus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "malignant uterine tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "malignant neoplasm of uterus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "CA - cancer of uterus", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" }, { "id": "DOID:363", "name": "uterus neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_363" } ] }, "evidence_source": [ { "id": "15571618", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/15571618", "evidence_list": [ { "evidence": "Uterine Adenosarcoma (UAS) with sarcomatous overgrowth stained strongly positive in five of eight (63%) cases. Pattern of strong positivity was focal in four of five (80%). These findings suggest that CD10 can be used to differentiate UAS from cellular leiomyoma, or in case endometrial stromal cells exhibit muscle differentiation. Furthermore, CD10 positivity in recurrent UAS might guide the pathologist toward an endometrial stromal origin." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "11532038", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/11532038", "evidence_list": [ { "evidence": "CD10 is a reliable and sensitive immunohistochemical marker of normal endometrial stroma. Positivity, which is often strong and/or diffuse is found in endometrial stromal nodules and low-grade ESS. Positive staining with CD10, when strong and diffuse, may be useful in distinguishing these tumours from histological mimics, especially cellular leiomyoma and AGCT which are generally negative. There was positive staining of all low-grade Endometrial stromal sarcoma (ESS)." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Immunohistochemical expression of CD10 antigen in uterine adenosarcoma.", "journal": "International journal of gynecological cancer : official journal of the International Gynecological Cancer Society", "authors": "Amant F, Steenkiste E, Schurmans K, Verbist L, Abeler VM, Tulunay G, de Jonge E, Massuger L, Moerman P, Vergote I", "date": "2004-12-02", "evidence": [], "reference": [ { "id": "15571618", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/15571618" } ] }, { "title": "CD10 is a sensitive and diagnostically useful immunohistochemical marker of normal endometrial stroma and of endometrial stromal neoplasms.", "journal": "Histopathology", "authors": "McCluggage WG, Sumathi VP, Maxwell P", "date": "2001-09-05", "evidence": [], "reference": [ { "id": "11532038", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/11532038" } ] } ], "biomarker_canonical_id": "AN6682", "score": 2.2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 1 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "c": "condition", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6683-1", "biomarker_component": [ { "biomarker": "increased CD274 level", "assessed_biomarker_entity": { "recommended_name": "Programmed cell death 1 ligand 1", "synonyms": [ { "synonym": "PD-L1" }, { "synonym": "PDCD1 ligand 1" }, { "synonym": "Programmed death ligand 1" }, { "synonym": "hPD-L1" }, { "synonym": "B7 homolog 1" }, { "synonym": "B7-H1" } ] }, "assessed_biomarker_entity_id": "UPKB:Q9NZQ7", "assessed_entity_type": "protein", "specimen": [ { "name": "stomach", "id": "UBERON:0000945", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000945", "loinc_code": "" } ], "evidence_source": [ { "id": "31981446", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31981446", "evidence_list": [ { "evidence": "Based on our established CTC detection platform, CTCs were isolated from peripheral blood samples collected from 70 patients (38 resectable and 32 unresectable) with GC using magnetic positive selection and a CSV-specific monoclonal antibody, 84-1. CSV+ PD-L1+ CTCs were observed in 50 of 70 (71%) GC patient samples, ranging from 0 to 261 mL-1. A higher number of CSV+ PD-L1+ CTCs were significantly associated with a short survival duration and poor therapeutic response. This study demonstrated that detection of PD-L1+ CTCs using a CSV-enrichment method has promising value as a clinically relevant prognostic marker for GC." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000945" } ] }, { "id": "30925913", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30925913", "evidence_list": [ { "evidence": "We found that inhibition of autophagy by pharmacological inhibitors or small interfering RNAs increased the levels of PD-L1 in cultured gastric cancer cells and in xenografts. Mechanistically, autophagy inhibition led to the accumulation of p62/SQSTM1 and activation of nuclear factor (NF)-kB, in which NF-kB inhibition or p62/SQSTM1 knockdown attenuated PD-L1 induction by autophagy inhibition. Immunohistochemical staining of primary tumor tissues of 137 patients with gastric cancer showed that LC3 and p62/SQSTM1 protein levels were positively correlated with PD-L1 (LC3, p < 0.001; p62/SQSTM1, p < 0.05). The expression of PD-L1 was also positively correlated with tumor lymphocyte infiltration (p < 0.001). We discovered that autophagy regulates PD-L1 expression in gastric cancer through the p62/SQSTM1-NF-kB pathway. Pharmacological modulation of autophagy may thus influence the therapeutic efficacy of PD-L1 blockade in gastric cancer." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000945" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" }, "synonyms": [ { "id": "DOID:10534", "name": "gastric neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" }, { "id": "DOID:10534", "name": "gastric cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" } ] }, "evidence_source": [ { "id": "31981446", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31981446", "evidence_list": [ { "evidence": "Based on our established CTC detection platform, CTCs were isolated from peripheral blood samples collected from 70 patients (38 resectable and 32 unresectable) with GC using magnetic positive selection and a CSV-specific monoclonal antibody, 84-1. CSV+ PD-L1+ CTCs were observed in 50 of 70 (71%) GC patient samples, ranging from 0 to 261 mL-1. A higher number of CSV+ PD-L1+ CTCs were significantly associated with a short survival duration and poor therapeutic response. This study demonstrated that detection of PD-L1+ CTCs using a CSV-enrichment method has promising value as a clinically relevant prognostic marker for GC." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "30925913", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30925913", "evidence_list": [ { "evidence": "We found that inhibition of autophagy by pharmacological inhibitors or small interfering RNAs increased the levels of PD-L1 in cultured gastric cancer cells and in xenografts. Mechanistically, autophagy inhibition led to the accumulation of p62/SQSTM1 and activation of nuclear factor (NF)-kB, in which NF-kB inhibition or p62/SQSTM1 knockdown attenuated PD-L1 induction by autophagy inhibition. Immunohistochemical staining of primary tumor tissues of 137 patients with gastric cancer showed that LC3 and p62/SQSTM1 protein levels were positively correlated with PD-L1 (LC3, p < 0.001; p62/SQSTM1, p < 0.05). The expression of PD-L1 was also positively correlated with tumor lymphocyte infiltration (p < 0.001). We discovered that autophagy regulates PD-L1 expression in gastric cancer through the p62/SQSTM1-NF-kB pathway. Pharmacological modulation of autophagy may thus influence the therapeutic efficacy of PD-L1 blockade in gastric cancer." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Prognostic significance of PD-L1 expression on cell-surface vimentin-positive circulating tumor cells in gastric cancer patients.", "journal": "Molecular oncology", "authors": "Liu M, Wang R, Sun X, Liu Y, Wang Z, Yan J, Kong X, Liang S, Liu Q, Zhao T, Ji X, Wang G, Wang F, Wang G, Chen L, Zhang Q, Lv W, Li H, Sun M", "date": "2020-01-26", "evidence": [], "reference": [ { "id": "31981446", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31981446" } ] }, { "title": "Autophagy inhibition enhances PD-L1 expression in gastric cancer.", "journal": "Journal of experimental & clinical cancer research : CR", "authors": "Wang X, Wu WKK, Gao J, Li Z, Dong B, Lin X, Li Y, Li Y, Gong J, Qi C, Peng Z, Yu J, Shen L", "date": "2019-03-31", "evidence": [], "reference": [ { "id": "30925913", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30925913" } ] } ], "biomarker_canonical_id": "AN6683", "score": 1.2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 1 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6683-2", "biomarker_component": [ { "biomarker": "increased CD274 level", "assessed_biomarker_entity": { "recommended_name": "Programmed cell death 1 ligand 1", "synonyms": [ { "synonym": "PD-L1" }, { "synonym": "PDCD1 ligand 1" }, { "synonym": "Programmed death ligand 1" }, { "synonym": "hPD-L1" }, { "synonym": "B7 homolog 1" }, { "synonym": "B7-H1" } ] }, "assessed_biomarker_entity_id": "UPKB:Q9NZQ7", "assessed_entity_type": "protein", "specimen": [ { "name": "kidney", "id": "UBERON:0002113", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0002113", "loinc_code": "" } ], "evidence_source": [ { "id": "31653140", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31653140", "evidence_list": [ { "evidence": "Among the 150 samples, 66 (44%) expressed PDL1 expression in the tumor cell surface, and a significant association was between the PDL1 expression and the high graded tumors" } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0002113" } ] }, { "id": "33797012", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/33797012", "evidence_list": [ { "evidence": "PD-L1 expression predicts response to immune checkpoint inhibitors in renal cell carcinomas (RCC), but has also been suggested to be linked to poor patient outcome." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0002113" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:263", "recommended_name": { "id": "DOID:263", "name": "kidney cancer", "description": "A urinary system cancer that is located_in the kidney.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_263" }, "synonyms": [ { "id": "DOID:263", "name": "malignant tumour of kidney", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_263" }, { "id": "DOID:263", "name": "malignant neoplasm of kidney except pelvis", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_263" }, { "id": "DOID:263", "name": "renal cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_263" } ] }, "evidence_source": [ { "id": "31653140", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31653140", "evidence_list": [ { "evidence": "Among the 150 samples, 66 (44%) expressed PDL1 expression in the tumor cell surface, and a significant association was between the PDL1 expression and the high graded tumors" } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "33797012", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/33797012", "evidence_list": [ { "evidence": "PD-L1 expression predicts response to immune checkpoint inhibitors in renal cell carcinomas (RCC), but has also been suggested to be linked to poor patient outcome." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Programmed Death Ligand 1; An Immunotarget for Renal Cell Carcinoma.", "journal": "Asian Pacific journal of cancer prevention : APJCP", "authors": "Chandrasekaran D, Sundaram S, N K, R P", "date": "2019-10-28", "evidence": [], "reference": [ { "id": "31653140", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31653140" } ] }, { "title": "Tumor cell PD-L1 expression is a strong predictor of unfavorable prognosis in immune checkpoint therapy-naive clear cell renal cell cancer.", "journal": "International urology and nephrology", "authors": "Möller K, Fraune C, Blessin NC, Lennartz M, Kluth M, Hube-Magg C, Lindhorst L, Dahlem R, Fisch M, Eichenauer T, Riechardt S, Simon R, Sauter G, Büscheck F, Höppner W, Matthies C, Doh O, Krech T, Marx AH, Zecha H, Rink M, Steurer S, Clauditz TS", "date": "2021-04-03", "evidence": [], "reference": [ { "id": "33797012", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/33797012" } ] } ], "biomarker_canonical_id": "AN6683", "score": 1.2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 1 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "c": "condition", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6684-1", "biomarker_component": [ { "biomarker": "increased ARPP-19 level", "assessed_biomarker_entity": { "recommended_name": "cAMP-regulated phosphoprotein 19", "synonyms": [ { "synonym": "ARPP-16" }, { "synonym": "ARPP-19" }, { "synonym": "ARPP16" }, { "synonym": "ENSAL" } ] }, "assessed_biomarker_entity_id": "NCBI: 10776", "assessed_entity_type": "gene", "specimen": [ { "name": "stomach", "id": "UBERON:0000945", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000945", "loinc_code": "" } ], "evidence_source": [ { "id": "32753897", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32753897", "evidence_list": [ { "evidence": "We observed ARPP-19 was up-regulated in Herceptin resistance gastric cancer cells NCI-N87-HR and MKN45-HR. The forced expression of ARPP-19 promoted, whereas the silencing of ARPP-19 impaired Herceptin resistance of HER2-positive gastric cancer cells both in vitro and in vivo. Moreover, ARPP-19 significantly enhanced the sphere formation capacity and CD44 expression, CD44 was also a positive factor of Herceptin resistance in HER2-positive gastric cancer cells. In addition, high level of ARPP-19 was positively associated with Herceptin resistance and poor survival rate of gastric cancer patients. We have demonstrated that ARPP-19 promoted Herceptin resistance of gastric cancer via up-regulation of CD44, our study suggested that ARPP-19 could be a potential diagnostic and therapeutic candidate for HER2-positive gastric cancer." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000945" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" }, "synonyms": [ { "id": "DOID:10534", "name": "gastric neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" }, { "id": "DOID:10534", "name": "gastric cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" } ] }, "evidence_source": [ { "id": "32753897", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32753897", "evidence_list": [ { "evidence": "We observed ARPP-19 was up-regulated in Herceptin resistance gastric cancer cells NCI-N87-HR and MKN45-HR. The forced expression of ARPP-19 promoted, whereas the silencing of ARPP-19 impaired Herceptin resistance of HER2-positive gastric cancer cells both in vitro and in vivo. Moreover, ARPP-19 significantly enhanced the sphere formation capacity and CD44 expression, CD44 was also a positive factor of Herceptin resistance in HER2-positive gastric cancer cells. In addition, high level of ARPP-19 was positively associated with Herceptin resistance and poor survival rate of gastric cancer patients. We have demonstrated that ARPP-19 promoted Herceptin resistance of gastric cancer via up-regulation of CD44, our study suggested that ARPP-19 could be a potential diagnostic and therapeutic candidate for HER2-positive gastric cancer." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "ARPP-19 Mediates Herceptin Resistance via Regulation of CD44 in Gastric Cancer.", "journal": "OncoTargets and therapy", "authors": "Gao X, Lu C, Chen C, Sun K, Liang Q, Shuai J, Wang X, Xu Y", "date": "2020-08-06", "evidence": [], "reference": [ { "id": "32753897", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32753897" } ] } ], "biomarker_canonical_id": "AN6684", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6685-1", "biomarker_component": [ { "biomarker": "increased DSC2 level", "assessed_biomarker_entity": { "recommended_name": "Desmocollin-2", "synonyms": [ { "synonym": "ARVD11" }, { "synonym": "CDHF2" }, { "synonym": "DG2" }, { "synonym": "DGII/III" }, { "synonym": "DSC3" } ] }, "assessed_biomarker_entity_id": "NCBI: 1824", "assessed_entity_type": "gene", "specimen": [ { "name": "stomach", "id": "UBERON:0000945", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000945", "loinc_code": "" } ], "evidence_source": [ { "id": "20527021", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/20527021", "evidence_list": [ { "evidence": "Gastric cancer (GC) is one of the most common malignancies worldwide. Genes expressed only in cancer tissue, and especially on the cell membrane, will be useful molecular markers for diagnosis and may also be good therapeutic targets. To identify genes that encode transmembrane proteins present in GC, we generated Escherichia coli ampicillin secretion trap (CAST) libraries from two GC cell lines and normal stomach. By sequencing 4320 colonies from CAST libraries, we identified 30 candidate genes that encode transmembrane proteins present in GC. Quantitative reverse transcription-polymerase chain reaction analysis of these candidates revealed that ZDHHC14, BST2, DRAM2, and DSC2 were expressed much more highly in GC than in 14 kinds of normal tissues. Among these, DSC2 encodes desmocollin 2, which is one of three known desmocollins. Immunohistochemical analysis demonstrated that 22 (28%) of 80 GC cases were positive for desmocollin 2, and desmocollin 2 expression was observed frequently in GC with the intestinal mucin phenotype. Furthermore, desmocollin 2 expression was correlated with CDX2 expression. These results suggest that expression of desmocollin 2, induced by CDX2, may be a key regulator for GC with the intestinal mucin phenotype. Our results provide a list of genes that have high potential as a diagnostic and therapeutic target for GC." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000945" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" }, "synonyms": [ { "id": "DOID:10534", "name": "gastric neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" }, { "id": "DOID:10534", "name": "gastric cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" } ] }, "evidence_source": [ { "id": "20527021", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/20527021", "evidence_list": [ { "evidence": "Gastric cancer (GC) is one of the most common malignancies worldwide. Genes expressed only in cancer tissue, and especially on the cell membrane, will be useful molecular markers for diagnosis and may also be good therapeutic targets. To identify genes that encode transmembrane proteins present in GC, we generated Escherichia coli ampicillin secretion trap (CAST) libraries from two GC cell lines and normal stomach. By sequencing 4320 colonies from CAST libraries, we identified 30 candidate genes that encode transmembrane proteins present in GC. Quantitative reverse transcription-polymerase chain reaction analysis of these candidates revealed that ZDHHC14, BST2, DRAM2, and DSC2 were expressed much more highly in GC than in 14 kinds of normal tissues. Among these, DSC2 encodes desmocollin 2, which is one of three known desmocollins. Immunohistochemical analysis demonstrated that 22 (28%) of 80 GC cases were positive for desmocollin 2, and desmocollin 2 expression was observed frequently in GC with the intestinal mucin phenotype. Furthermore, desmocollin 2 expression was correlated with CDX2 expression. These results suggest that expression of desmocollin 2, induced by CDX2, may be a key regulator for GC with the intestinal mucin phenotype. Our results provide a list of genes that have high potential as a diagnostic and therapeutic target for GC." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Search for transmembrane protein in gastric cancer by the Escherichia coli ampicillin secretion trap: expression of DSC2 in gastric cancer with intestinal phenotype.", "journal": "The Journal of pathology", "authors": "Anami K, Oue N, Noguchi T, Sakamoto N, Sentani K, Hayashi T, Hinoi T, Okajima M, Graff JM, Yasui W", "date": "2010-06-09", "evidence": [], "reference": [ { "id": "20527021", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/20527021" } ] } ], "biomarker_canonical_id": "AN6685", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6686-1", "biomarker_component": [ { "biomarker": "increased HOXA10 level", "assessed_biomarker_entity": { "recommended_name": "Homeobox protein HOXA10", "synonyms": [ { "synonym": "Homeobox protein Hox-1.8" }, { "synonym": "Homeobox protein Hox-1H" }, { "synonym": "PL" } ] }, "assessed_biomarker_entity_id": "UPKB:P31260", "assessed_entity_type": "protein", "specimen": [ { "name": "stomach", "id": "UBERON:0000945", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000945", "loinc_code": "" } ], "evidence_source": [ { "id": "31406476", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31406476", "evidence_list": [ { "evidence": "HOXA10 expression was obviously increased in gastric cancer tissues and cells when compared with the normal gastric tissue samples and cells. Upregulation of HOXA10 significantly enhanced cell proliferation, cloning formation and tumorigenesis abilities and reduced cell apoptosis in gastric cancer, and promoted the activation of JAK1/STAT3 signaling." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000945" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" }, "synonyms": [ { "id": "DOID:10534", "name": "gastric neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" }, { "id": "DOID:10534", "name": "gastric cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" } ] }, "evidence_source": [ { "id": "31406476", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31406476", "evidence_list": [ { "evidence": "HOXA10 expression was obviously increased in gastric cancer tissues and cells when compared with the normal gastric tissue samples and cells. Upregulation of HOXA10 significantly enhanced cell proliferation, cloning formation and tumorigenesis abilities and reduced cell apoptosis in gastric cancer, and promoted the activation of JAK1/STAT3 signaling." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "HOXA10 deteriorates gastric cancer through activating JAK1/STAT3 signaling pathway.", "journal": "Cancer management and research", "authors": "Chen W, Wu G, Zhu Y, Zhang W, Zhang H, Zhou Y, Sun P", "date": "2019-08-14", "evidence": [], "reference": [ { "id": "31406476", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31406476" } ] } ], "biomarker_canonical_id": "AN6686", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6687-1", "biomarker_component": [ { "biomarker": "decreased OLFM4 level", "assessed_biomarker_entity": { "recommended_name": "Olfactomedin-4", "synonyms": [ { "synonym": "GC1" }, { "synonym": "GW112" }, { "synonym": "OLM4" }, { "synonym": "OlfD" }, { "synonym": "UNQ362" }, { "synonym": "bA209J19.1" }, { "synonym": "hGC-1" }, { "synonym": "hOLfD" }, { "synonym": "pDP4" } ] }, "assessed_biomarker_entity_id": "NCBI: 10562", "assessed_entity_type": "gene", "specimen": [ { "name": "stomach", "id": "UBERON:0000945", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000945", "loinc_code": "" } ], "evidence_source": [ { "id": "22471589", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/22471589", "evidence_list": [ { "evidence": "Our study suggests that depletion of OLFM4 significantly inhibits tumorigenicity of the gastric cancer SGC-7901 and MKN45 cells. Blocking OLFM4 expression can sensitize gastric cancer cells to H2O2 or TNF alpha treatment by increasing caspase-3 dependent apoptosis. The elimination of OLFM4 protein by RNA interference in SGC-7901 and MKN45 cells significantly inhibits tumorigenicity both in vitro and in vivo by induction of cell G1 arrest (all P < 0.01). OLFM4 knockdown did not trigger obvious cell apoptosis but increased H2O2 or TNF alpha-induced apoptosis and caspase-3 activity (all P < 0.01)." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000945" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" }, "synonyms": [ { "id": "DOID:10534", "name": "gastric neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" }, { "id": "DOID:10534", "name": "gastric cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" } ] }, "evidence_source": [ { "id": "22471589", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/22471589", "evidence_list": [ { "evidence": "Our study suggests that depletion of OLFM4 significantly inhibits tumorigenicity of the gastric cancer SGC-7901 and MKN45 cells. Blocking OLFM4 expression can sensitize gastric cancer cells to H2O2 or TNF alpha treatment by increasing caspase-3 dependent apoptosis. The elimination of OLFM4 protein by RNA interference in SGC-7901 and MKN45 cells significantly inhibits tumorigenicity both in vitro and in vivo by induction of cell G1 arrest (all P < 0.01). OLFM4 knockdown did not trigger obvious cell apoptosis but increased H2O2 or TNF alpha-induced apoptosis and caspase-3 activity (all P < 0.01)." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Depletion of OLFM4 gene inhibits cell growth and increases sensitization to hydrogen peroxide and tumor necrosis factor-alpha induced-apoptosis in gastric cancer cells.", "journal": "Journal of biomedical science", "authors": "Liu RH, Yang MH, Xiang H, Bao LM, Yang HA, Yue LW, Jiang X, Ang N, Wu LY, Huang Y", "date": "2012-04-05", "evidence": [], "reference": [ { "id": "22471589", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/22471589" } ] } ], "biomarker_canonical_id": "AN6687", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "w": "weight", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6688-1", "biomarker_component": [ { "biomarker": "increased MUC13 level", "assessed_biomarker_entity": { "recommended_name": "Mucin-13", "synonyms": [ { "synonym": "MUC-13" }, { "synonym": "Down-regulated in colon cancer 1" } ] }, "assessed_biomarker_entity_id": "UPKB:Q9H3R2", "assessed_entity_type": "protein", "specimen": [ { "name": "stomach", "id": "UBERON:0000945", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000945", "loinc_code": "" } ], "evidence_source": [ { "id": "20398667", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/20398667", "evidence_list": [ { "evidence": "Expression of CDH17 or MUC13 correlated with patient survival in the test and validation sets. Multivariate analysis showed that CDH17 was an independent prognostic factor in patients with stage I or node-negative disease. Expression of CDH17 and MUC13 was up-regulated in gastric cancer tissues. CDH17 is a promising prognostic marker for early stage gastric cancer." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000945" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" }, "synonyms": [ { "id": "DOID:10534", "name": "gastric neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" }, { "id": "DOID:10534", "name": "gastric cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" } ] }, "evidence_source": [ { "id": "20398667", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/20398667", "evidence_list": [ { "evidence": "Expression of CDH17 or MUC13 correlated with patient survival in the test and validation sets. Multivariate analysis showed that CDH17 was an independent prognostic factor in patients with stage I or node-negative disease. Expression of CDH17 and MUC13 was up-regulated in gastric cancer tissues. CDH17 is a promising prognostic marker for early stage gastric cancer." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Gene expression profiling of metaplastic lineages identifies CDH17 as a prognostic marker in early stage gastric cancer.", "journal": "Gastroenterology", "authors": "Lee HJ, Nam KT, Park HS, Kim MA, Lafleur BJ, Aburatani H, Yang HK, Kim WH, Goldenring JR", "date": "2010-04-20", "evidence": [], "reference": [ { "id": "20398667", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/20398667" } ] } ], "biomarker_canonical_id": "AN6688", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6689-1", "biomarker_component": [ { "biomarker": "increased CDH17 level", "assessed_biomarker_entity": { "recommended_name": "Cadherin-17", "synonyms": [ { "synonym": "Intestinal peptide-associated transporter HPT-1" }, { "synonym": "Liver-intestine cadherin" }, { "synonym": "LI-cadherin" } ] }, "assessed_biomarker_entity_id": "UPKB:Q12864", "assessed_entity_type": "protein", "specimen": [ { "name": "stomach", "id": "UBERON:0000945", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000945", "loinc_code": "" } ], "evidence_source": [ { "id": "20398667", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/20398667", "evidence_list": [ { "evidence": "Expression of CDH17 or MUC13 correlated with patient survival in the test and validation sets. Multivariate analysis showed that CDH17 was an independent prognostic factor in patients with stage I or node-negative disease. Expression of CDH17 and MUC13 was up-regulated in gastric cancer tissues. CDH17 is a promising prognostic marker for early stage gastric cancer." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000945" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" }, "synonyms": [ { "id": "DOID:10534", "name": "gastric neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" }, { "id": "DOID:10534", "name": "gastric cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" } ] }, "evidence_source": [ { "id": "20398667", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/20398667", "evidence_list": [ { "evidence": "Expression of CDH17 or MUC13 correlated with patient survival in the test and validation sets. Multivariate analysis showed that CDH17 was an independent prognostic factor in patients with stage I or node-negative disease. Expression of CDH17 and MUC13 was up-regulated in gastric cancer tissues. CDH17 is a promising prognostic marker for early stage gastric cancer." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Gene expression profiling of metaplastic lineages identifies CDH17 as a prognostic marker in early stage gastric cancer.", "journal": "Gastroenterology", "authors": "Lee HJ, Nam KT, Park HS, Kim MA, Lafleur BJ, Aburatani H, Yang HK, Kim WH, Goldenring JR", "date": "2010-04-20", "evidence": [], "reference": [ { "id": "20398667", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/20398667" } ] } ], "biomarker_canonical_id": "AN6689", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "f": "frequency", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6690-1", "biomarker_component": [ { "biomarker": "increased PVT1 level", "assessed_biomarker_entity": { "recommended_name": "Plasmacytoma variant translocation 1", "synonyms": [] }, "assessed_biomarker_entity_id": "RNAC:URS0000D3E92F", "assessed_entity_type": "RNA", "specimen": [ { "name": "stomach", "id": "UBERON:0000945", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000945", "loinc_code": "" } ], "evidence_source": [ { "id": "31966056", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31966056", "evidence_list": [ { "evidence": "Compared with paracancerous tissues, the expression of PVT1 and miR-125 was significantly increased in gastric cancer tissues. There were no significant differences in the expression level of PVT1 between gastric cancer patients of different genders and ages. The higher the gastric cancer staging was, the more obvious the expression level of PVT1 in the tissues of patients with gastric cancer was, and the more obvious the expression of PVT1 in the tissues of patients with gastric lymph node metastasis was." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000945" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" }, "synonyms": [ { "id": "DOID:10534", "name": "gastric neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" }, { "id": "DOID:10534", "name": "gastric cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" } ] }, "evidence_source": [ { "id": "31966056", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31966056", "evidence_list": [ { "evidence": "Compared with paracancerous tissues, the expression of PVT1 and miR-125 was significantly increased in gastric cancer tissues. There were no significant differences in the expression level of PVT1 between gastric cancer patients of different genders and ages. The higher the gastric cancer staging was, the more obvious the expression level of PVT1 in the tissues of patients with gastric cancer was, and the more obvious the expression of PVT1 in the tissues of patients with gastric lymph node metastasis was." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Regulation of lncRNA PVT1 on miR-125 in metastasis of gastric cancer cells.", "journal": "Oncology letters", "authors": "Niu J, Song X, Zhang X", "date": "2020-01-23", "evidence": [], "reference": [ { "id": "31966056", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31966056" } ] } ], "biomarker_canonical_id": "AN6690", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "f": "frequency", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6691-1", "biomarker_component": [ { "biomarker": "decreased PRMT1 level", "assessed_biomarker_entity": { "recommended_name": "Protein arginine methyltransferase-1", "synonyms": [ { "synonym": "Histone-arginine N-methyltransferase PRMT1" }, { "synonym": "Interferon receptor 1-bound protein 4" } ] }, "assessed_biomarker_entity_id": "UPKB:Q99873", "assessed_entity_type": "protein", "specimen": [ { "name": "kidney", "id": "UBERON:0002113", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0002113", "loinc_code": "" } ], "evidence_source": [ { "id": "31655611", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31655611", "evidence_list": [ { "evidence": "Nuclear PRMT1 IHC expression was seen in all samples of the renal parenchyma used as a positive control. PRMT1 expression together with low-nuclear tumor grade and stage were significantly associated with better cancer-specific survival (p = 0.029). Patients who died of clear cell Renal Cell Carcinoma (ccRCC) showed homogenous loss of PRMT1 in 44.7%." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0002113" } ] }, { "id": "33859753", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/33859753", "evidence_list": [ { "evidence": "Taken together, our study revealed a PRMT1-dependent epigenetic mechanism in the control of clear cell renal cell carcinoma (ccRCC) tumor growth and drug resistance, indicating PRMT1 may serve as a promising target for therapeutic intervention in ccRCC patients." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0002113" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:263", "recommended_name": { "id": "DOID:263", "name": "kidney cancer", "description": "A urinary system cancer that is located_in the kidney.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_263" }, "synonyms": [ { "id": "DOID:263", "name": "malignant tumour of kidney", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_263" }, { "id": "DOID:263", "name": "malignant neoplasm of kidney except pelvis", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_263" }, { "id": "DOID:263", "name": "renal cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_263" } ] }, "evidence_source": [ { "id": "31655611", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31655611", "evidence_list": [ { "evidence": "Nuclear PRMT1 IHC expression was seen in all samples of the renal parenchyma used as a positive control. PRMT1 expression together with low-nuclear tumor grade and stage were significantly associated with better cancer-specific survival (p = 0.029). Patients who died of clear cell Renal Cell Carcinoma (ccRCC) showed homogenous loss of PRMT1 in 44.7%." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "33859753", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/33859753", "evidence_list": [ { "evidence": "Taken together, our study revealed a PRMT1-dependent epigenetic mechanism in the control of clear cell renal cell carcinoma (ccRCC) tumor growth and drug resistance, indicating PRMT1 may serve as a promising target for therapeutic intervention in ccRCC patients." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "PRMT1 expression in renal cell tumors- application in differential diagnosis and prognostic relevance.", "journal": "Diagnostic pathology", "authors": "Filipović J, Bosić M, Ćirović S, Životić M, Dunđerović D, Đorđević D, Živković-Perišić S, Lipkovski A, Marković-Lipkovski J", "date": "2019-10-28", "evidence": [], "reference": [ { "id": "31655611", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31655611" } ] }, { "title": "PRMT1 is a novel molecular therapeutic target for clear cell renal cell carcinoma.", "journal": "Theranostics", "authors": "Wang J, Wang C, Xu P, Li X, Lu Y, Jin D, Yin X, Jiang H, Huang J, Xiong H, Ye F, Jin J, Chen Y, Xie Y, Chen Z, Ding H, Zhang H, Liu R, Jiang H, Chen K, Yao Z, Luo C, Huang Y, Zhang Y, Zhang J", "date": "2021-04-17", "evidence": [], "reference": [ { "id": "33859753", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/33859753" } ] } ], "biomarker_canonical_id": "AN6691", "score": 1.2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 1 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6692-1", "biomarker_component": [ { "biomarker": "increased NUPR1 level", "assessed_biomarker_entity": { "recommended_name": "Nuclear protein 1", "synonyms": [ { "synonym": "Candidate of metastasis 1" }, { "synonym": "Protein p8" } ] }, "assessed_biomarker_entity_id": "UPKB:O60356", "assessed_entity_type": "protein", "specimen": [ { "name": "kidney", "id": "UBERON:0002113", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0002113", "loinc_code": "" } ], "evidence_source": [ { "id": "34030133", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/34030133", "evidence_list": [ { "evidence": "NUPR1 mRNA levels were significantly increased in ccRCC cells and cancer tissues compared with HK-2 cells (human renal cortex/proximal tubular epithelial cells) and adjacent normal kidney tissues. High NUPR1 mRNA level in primary tumors was correlated with poor overall survival (OS) and disease-free survival (DFS)." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0002113" } ] }, { "id": "27451286", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/27451286", "evidence_list": [ { "evidence": "Finally, immunohistochemical analysis revealed strong expression of NUPR1 in the nuclei of renal proximal tubules of injured human kidney allografts, but not in those of stable allografts. Taken together, these results suggest that epithelial expression of NUPR1 has a protective role in response to injury after renal transplant and, presumably, in other forms of acute tubular damage." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0002113" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:263", "recommended_name": { "id": "DOID:263", "name": "kidney cancer", "description": "A urinary system cancer that is located_in the kidney.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_263" }, "synonyms": [ { "id": "DOID:263", "name": "malignant tumour of kidney", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_263" }, { "id": "DOID:263", "name": "malignant neoplasm of kidney except pelvis", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_263" }, { "id": "DOID:263", "name": "renal cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_263" } ] }, "evidence_source": [ { "id": "34030133", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/34030133", "evidence_list": [ { "evidence": "NUPR1 mRNA levels were significantly increased in ccRCC cells and cancer tissues compared with HK-2 cells (human renal cortex/proximal tubular epithelial cells) and adjacent normal kidney tissues. High NUPR1 mRNA level in primary tumors was correlated with poor overall survival (OS) and disease-free survival (DFS)." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "27451286", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/27451286", "evidence_list": [ { "evidence": "Finally, immunohistochemical analysis revealed strong expression of NUPR1 in the nuclei of renal proximal tubules of injured human kidney allografts, but not in those of stable allografts. Taken together, these results suggest that epithelial expression of NUPR1 has a protective role in response to injury after renal transplant and, presumably, in other forms of acute tubular damage." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "NUPR1 is a novel potential biomarker and confers resistance to sorafenib in clear cell renal cell carcinoma by increasing stemness and targeting the PTEN/AKT/mTOR pathway.", "journal": "Aging", "authors": "He W, Cheng F, Zheng B, Wang J, Zhao G, Yao Z, Zhang T", "date": "2021-05-25", "evidence": [], "reference": [ { "id": "34030133", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/34030133" } ] }, { "title": "Stress Response Gene Nupr1 Alleviates Cyclosporin A Nephrotoxicity In Vivo.", "journal": "Journal of the American Society of Nephrology : JASN", "authors": "Galichon P, Bataille A, Vandermeersch S, Wetzstein M, Xu-Dubois YC, Legouis D, Hertig A, Buob D, Placier S, Bigé N, Lefevre G, Jouanneau C, Martin C, Iovanna JL, Rondeau E", "date": "2016-07-28", "evidence": [], "reference": [ { "id": "27451286", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/27451286" } ] } ], "biomarker_canonical_id": "AN6692", "score": 1.2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 1 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "c": "condition", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6693-1", "biomarker_component": [ { "biomarker": "increased DKC1 level", "assessed_biomarker_entity": { "recommended_name": "H/ACA ribonucleoprotein complex subunit", "synonyms": [ { "synonym": "CBF5 homolog" }, { "synonym": "Dyskerin" }, { "synonym": "Nopp140-associated protein of 57 kDa" }, { "synonym": "Nucleolar 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"condition": { "id": "DOID:263", "recommended_name": { "id": "DOID:263", "name": "kidney cancer", "description": "A urinary system cancer that is located_in the kidney.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_263" }, "synonyms": [ { "id": "DOID:263", "name": "malignant tumour of kidney", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_263" }, { "id": "DOID:263", "name": "malignant neoplasm of kidney except pelvis", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_263" }, { "id": "DOID:263", "name": "renal cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_263" } ] }, "evidence_source": [ { "id": "29901172", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/29901172", "evidence_list": [ { "evidence": "High DKC1 expression was detected in 61.3% ccRCC tissues and 34.7% paracancerous tissues. ccRCC patients with high DKC1 expression were correlated with greater unfavorable 5-year overall and disease-specific survival than the rest of the patients with low DKC1 expression (P<0.001 and P<0.001, respectively)." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "DKC1 serves as a potential prognostic biomarker for human clear cell renal cell carcinoma and promotes its proliferation, migration and invasion via the NF‑κB pathway.", "journal": "Oncology reports", "authors": "Zhang M, Pan Y, Jiang R, Hou P, Shan H, Chen F, Jiang T, Bai J, Zheng J", "date": "2018-06-15", "evidence": [], "reference": [ { "id": "29901172", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/29901172" } ] } ], "biomarker_canonical_id": "AN6693", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { 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significantly increased in ccRCC tissues compared with normal matched tissues. Patients with tumors that expressed high levels of SR-BI had a shorter PFS survival (P = 0.0062)." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0002113" } ] }, { "id": "26936883", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/26936883", "evidence_list": [ { "evidence": "Our findings demonstrate that hSR-BII, and to a lesser extent hSR-BI, significantly increase LPS-induced inflammation and contribute to LPS-induced tissue injury in the liver and kidney, two major organs susceptible to LPS toxicity." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0002113" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:263", "recommended_name": { "id": "DOID:263", "name": "kidney cancer", "description": "A urinary system cancer that is located_in the kidney.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_263" }, "synonyms": [ { "id": "DOID:263", "name": "malignant tumour of kidney", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_263" }, { "id": "DOID:263", "name": "malignant neoplasm of kidney except pelvis", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_263" }, { "id": "DOID:263", "name": "renal cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_263" } ] }, "evidence_source": [ { "id": "29357836", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/29357836", "evidence_list": [ { "evidence": "The expression of SR-BI was significantly increased in ccRCC tissues compared with normal matched tissues. Patients with tumors that expressed high levels of SR-BI had a shorter PFS survival (P = 0.0062)." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "26936883", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/26936883", "evidence_list": [ { "evidence": "Our findings demonstrate that hSR-BII, and to a lesser extent hSR-BI, significantly increase LPS-induced inflammation and contribute to LPS-induced tissue injury in the liver and kidney, two major organs susceptible to LPS toxicity." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Up-regulation of SR-BI promotes progression and serves as a prognostic biomarker in clear cell renal cell carcinoma.", "journal": "BMC cancer", "authors": "Xu GH, Lou N, Shi HC, Xu YC, Ruan HL, Xiao W, Liu L, Li X, Xiao HB, Qiu B, Bao L, Yuan CF, Zhou YL, Hu WJ, Chen K, Yang HM, Zhang XP", "date": "2018-01-24", "evidence": [], "reference": [ { "id": "29357836", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/29357836" } ] }, { "title": "Human SR-BI and SR-BII Potentiate Lipopolysaccharide-Induced Inflammation and Acute Liver and Kidney Injury in Mice.", "journal": "Journal of immunology (Baltimore, Md. : 1950)", "authors": "Baranova IN, Souza AC, Bocharov AV, Vishnyakova TG, Hu X, Vaisman BL, Amar MJ, Chen Z, Kost Y, Remaley AT, Patterson AP, Yuen PS, Star RA, Eggerman TL", "date": "2016-03-05", "evidence": [], "reference": [ { "id": "26936883", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/26936883" } ] } ], "biomarker_canonical_id": "AN6694", "score": 1.2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 1 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "w": "weight", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6695-1", "biomarker_component": [ { "biomarker": "decreased QKI level", "assessed_biomarker_entity": { "recommended_name": "Protein quaking", "synonyms": [ { "synonym": "Protein quaking" }, { "synonym": "Hqk" }, { "synonym": "HqkI" } ] }, "assessed_biomarker_entity_id": "UPKB:Q96PU8", "assessed_entity_type": "protein", "specimen": [ { "name": "kidney", "id": "UBERON:0002113", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0002113", "loinc_code": "" } ], "evidence_source": [ { "id": "27767378", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/27767378", "evidence_list": [ { "evidence": "The relative expression level of QKI-5 was significantly lower in the tumor tissues than it was in their noncancerous counterparts (P < 0.01). 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Decreased QKI-5 expression significantly correlated with poorer overall survival in ccRCC patients." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "34804823", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/34804823", "evidence_list": [ { "evidence": "Our results revealed that downregulation of QKI-5 by miR-200c attenuated KIRC migration and invasion via the EMT process, indicating that QKI-5 may be a potential therapeutic target and a key indicator of kidney renal clear cell carcinoma (KIRC) progression." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "RNA-binding protein QKI-5 inhibits the proliferation of clear cell renal cell carcinoma via post-transcriptional stabilization of RASA1 mRNA.", "journal": "Cell cycle (Georgetown, Tex.)", "authors": "Zhang RL, Yang JP, Peng LX, Zheng LS, Xie P, Wang MY, Cao Y, Zhang ZL, Zhou FJ, Qian CN, Bao YX", "date": "2016-10-22", "evidence": [], "reference": [ { "id": "27767378", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/27767378" } ] }, { "title": "Quaking I-5 protein inhibits invasion and migration of kidney renal clear cell carcinoma via inhibiting epithelial-mesenchymal transition suppression through the regulation of microRNA 200c.", "journal": "Translational andrology and urology", "authors": "Zhang R, Wang W, Aimudula A, Lu S, Lu P, Aihaiti R, Bao Y", "date": "2021-11-23", "evidence": [], "reference": [ { "id": "34804823", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/34804823" } ] } ], "biomarker_canonical_id": "AN6695", "score": 1.2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 1 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "f": "frequency", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6696-1", "biomarker_component": [ { "biomarker": "decreased SORBS2 level", "assessed_biomarker_entity": { "recommended_name": "Sorbin and SH3 domain-containing protein 2", "synonyms": [ { "synonym": "Arg-binding protein 2" }, { "synonym": "ArgBP2" }, { "synonym": "Arg/Abl-interacting protein 2" }, { "synonym": "Sorbin" } ] }, "assessed_biomarker_entity_id": "UPKB:O94875", "assessed_entity_type": "protein", "specimen": [ { "name": "kidney", "id": "UBERON:0002113", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0002113", "loinc_code": "" } ], "evidence_source": [ { "id": "33311452", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/33311452", "evidence_list": [ { "evidence": "There was significantly lower expression of SORBS2 protein in metastatic tissues than that in primary tissues and normal tissues. Kaplan‚ÄìMeier survival analysis indicated that patients with low SORBS2 had a poorer overall survival than those belonging to high SORBS2 levels in ccRCC." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0002113" } ] }, { "id": "32905431", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32905431", "evidence_list": [ { "evidence": "KCNQ1OT1 and SORBS2 were elevated in DN. 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Kaplan‚ÄìMeier survival analysis indicated that patients with low SORBS2 had a poorer overall survival than those belonging to high SORBS2 levels in ccRCC." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32905431", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32905431", "evidence_list": [ { "evidence": "KCNQ1OT1 and SORBS2 were elevated in DN. Both knockdown of KCNQ1OT1 and silencing of SORBS2 restrained proliferation and fibrosis and induced apoptosis in diabetic nephropathy (DN) cells." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "RNA-binding protein SORBS2 suppresses clear cell renal cell carcinoma metastasis by enhancing MTUS1 mRNA stability.", "journal": "Cell death & disease", "authors": "Lv Q, Dong F, Zhou Y, Cai Z, Wang G", "date": "2020-12-15", "evidence": [], "reference": [ { "id": "33311452", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/33311452" } ] }, { "title": "LncRNA KCNQ1OT1 affects cell proliferation, apoptosis and fibrosis through regulating miR-18b-5p/SORBS2 axis and NF-ĸB pathway in diabetic nephropathy.", "journal": "Diabetology & metabolic syndrome", "authors": "Jie R, Zhu P, Zhong J, Zhang Y, Wu H", "date": "2020-09-10", "evidence": [], "reference": [ { "id": "32905431", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32905431" } ] } ], "biomarker_canonical_id": "AN6696", "score": 1.2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 1 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "w": "weight", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6697-1", "biomarker_component": [ { "biomarker": "increased IGF2BP3 level", "assessed_biomarker_entity": { "recommended_name": "Insulin-like growth factor 2 mRNA-binding protein 3", "synonyms": [ { "synonym": "IGF2 mRNA-binding protein 3" }, { "synonym": "IMP-3" }, { "synonym": "IGF-II mRNA-binding protein 3" }, { "synonym": "KH domain-containing protein overexpressed in cancer" }, { "synonym": "hKOC" }, { "synonym": "VICKZ family member 3" } ] }, "assessed_biomarker_entity_id": "UPKB:O00425", "assessed_entity_type": "protein", "specimen": [ { "name": "kidney", "id": "UBERON:0002113", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0002113", "loinc_code": "" } ], "evidence_source": [ { "id": "30650187", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30650187", "evidence_list": [ { "evidence": "IMP3 concentration was significantly elevated in plasma samples of tumor patients compared to healthy controls (p=0.015). IMP3 mRNA expression was significantly higher in Renal Cell Carcinoma (RCC) tissues compared to tumor neighboring normal tissues (p=0.001). high IMP3 plasma concentration was an independent risk factor of Overall Survival, OS, (p=0.002) and DSS (p=0.039) and elevated IMP3 mRNA expression levels were independently associated with poor DSS (p=0.047)." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0002113" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:263", "recommended_name": { "id": "DOID:263", "name": "kidney cancer", "description": "A urinary system cancer that is located_in the kidney.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_263" }, "synonyms": [ { "id": "DOID:263", "name": "malignant tumour of kidney", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_263" }, { "id": "DOID:263", "name": "malignant neoplasm of kidney except pelvis", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_263" }, { "id": "DOID:263", "name": "renal cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_263" } ] }, "evidence_source": [ { "id": "30650187", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30650187", "evidence_list": [ { "evidence": "IMP3 concentration was significantly elevated in plasma samples of tumor patients compared to healthy controls (p=0.015). IMP3 mRNA expression was significantly higher in Renal Cell Carcinoma (RCC) tissues compared to tumor neighboring normal tissues (p=0.001). high IMP3 plasma concentration was an independent risk factor of Overall Survival, OS, (p=0.002) and DSS (p=0.039) and elevated IMP3 mRNA expression levels were independently associated with poor DSS (p=0.047)." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Circulating and tissue IMP3 levels are correlated with poor survival in renal cell carcinoma.", "journal": "International journal of cancer", "authors": "Tschirdewahn S, Panic A, Püllen L, Harke NN, Hadaschik B, Riesz P, Horváth A, Szalontai J, Nyirády P, Baba HA, Reis H, Szarvas T", "date": "2019-01-17", "evidence": [], "reference": [ { "id": "30650187", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30650187" } ] } ], "biomarker_canonical_id": "AN6697", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6698-1", "biomarker_component": [ { "biomarker": "increased APOC1 level", "assessed_biomarker_entity": { "recommended_name": "Apolipoprotein C-I", "synonyms": [ { "synonym": "Apo-CI" }, { "synonym": "ApoC-I" }, { "synonym": "Apolipoprotein C1" } ] }, "assessed_biomarker_entity_id": "UPKB:P02654", "assessed_entity_type": "protein", "specimen": [ { "name": "stomach", "id": "UBERON:0000945", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000945", "loinc_code": "" } ], "evidence_source": [ { "id": "31555694", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31555694", "evidence_list": [ { "evidence": "It was firstly found that concentration of APOC1 in serum was significantly higher in GC than that in control. Expression of APOC1 protein was also higher in GC than that in adjacent issues of GC and normal tissues using tissues array by immunohistochemistry." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000945" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" }, "synonyms": [ { "id": "DOID:10534", "name": "gastric neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" }, { "id": "DOID:10534", "name": "gastric cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" } ] }, "evidence_source": [ { "id": "31555694", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31555694", "evidence_list": [ { "evidence": "It was firstly found that concentration of APOC1 in serum was significantly higher in GC than that in control. Expression of APOC1 protein was also higher in GC than that in adjacent issues of GC and normal tissues using tissues array by immunohistochemistry." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Apolipoprotein C1 (APOC1) as a novel diagnostic and prognostic biomarker for gastric cancer.", "journal": "Annals of translational medicine", "authors": "Yi J, Ren L, Wu J, Li W, Zheng X, Du G, Wang J", "date": "2019-09-27", "evidence": [], "reference": [ { "id": "31555694", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31555694" } ] } ], "biomarker_canonical_id": "AN6698", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6699-1", "biomarker_component": [ { "biomarker": "decreased ATP4B level", "assessed_biomarker_entity": { "recommended_name": "Potassium-transporting ATPase subunit beta", "synonyms": [ { "synonym": "ATP6B" } ] }, "assessed_biomarker_entity_id": "NCBI: 496", "assessed_entity_type": "gene", "specimen": [ { "name": "stomach", "id": "UBERON:0000945", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000945", "loinc_code": "" } ], "evidence_source": [ { "id": "28281974", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/28281974", "evidence_list": [ { "evidence": "ATP4B expression was decreased in human GC tissues and cell lines associated with DNA hypermethylation and histone hypoacetylation of histone H3 lysine 9 at its intragenic region close to the transcriptional start site." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000945" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" }, "synonyms": [ { "id": "DOID:10534", "name": "gastric neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" }, { "id": "DOID:10534", "name": "gastric cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" } ] }, "evidence_source": [ { "id": "28281974", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/28281974", "evidence_list": [ { "evidence": "ATP4B expression was decreased in human GC tissues and cell lines associated with DNA hypermethylation and histone hypoacetylation of histone H3 lysine 9 at its intragenic region close to the transcriptional start site." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Silencing of ATP4B of ATPase H", "journal": "Oncology research", "authors": "Lin S, Lin B, Wang X, Pan Y, Xu Q, He JS, Gong W, Xing R, He Y, Guo L, Lu Y, Wang JM, Huang J", "date": "2017-03-11", "evidence": [], "reference": [ { "id": "28281974", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/28281974" } ] } ], "biomarker_canonical_id": "AN6699", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "f": "frequency", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6700-1", "biomarker_component": [ { "biomarker": "increased DDX5 level", "assessed_biomarker_entity": { "recommended_name": "Probable ATP-dependent RNA helicase", "synonyms": [ { "synonym": "DEAD box protein 5" }, { "synonym": "RNA helicase p68" } ] }, "assessed_biomarker_entity_id": "UPKB:P17844", "assessed_entity_type": "protein", "specimen": [ { "name": "stomach", "id": "UBERON:0000945", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000945", "loinc_code": "" } ], "evidence_source": [ { "id": "28216662", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/28216662", "evidence_list": [ { "evidence": "In this study, we observed that DDX5 was significantly up-regulated in gastric cancer tissues compared with the paired adjacent normal tissues. The expression of DDX5 correlated strongly with Ki67 index and pathological stage of gastric cancer. In vitro and in vivo studies suggested that knockdown of DDX5 inhibited gastric cancer cell proliferation, colony formation and xenografts growth, whereas ectopic expression of DDX5 promoted these cellular functions." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000945" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" }, "synonyms": [ { "id": "DOID:10534", "name": "gastric neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" }, { "id": "DOID:10534", "name": "gastric cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" } ] }, "evidence_source": [ { "id": "28216662", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/28216662", "evidence_list": [ { "evidence": "In this study, we observed that DDX5 was significantly up-regulated in gastric cancer tissues compared with the paired adjacent normal tissues. The expression of DDX5 correlated strongly with Ki67 index and pathological stage of gastric cancer. In vitro and in vivo studies suggested that knockdown of DDX5 inhibited gastric cancer cell proliferation, colony formation and xenografts growth, whereas ectopic expression of DDX5 promoted these cellular functions." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "DDX5 promotes gastric cancer cell proliferation in vitro and in vivo through mTOR signaling pathway.", "journal": "Scientific reports", "authors": "Du C, Li DQ, Li N, Chen L, Li SS, Yang Y, Hou MX, Xie MJ, Zheng ZD", "date": "2017-02-22", "evidence": [], "reference": [ { "id": "28216662", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/28216662" } ] } ], "biomarker_canonical_id": "AN6700", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "w": "weight", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6701-1", "biomarker_component": [ { "biomarker": "increased GPX1 level", "assessed_biomarker_entity": { "recommended_name": "Glutathione peroxidase 1", "synonyms": [ { "synonym": "GPx-1" }, { "synonym": "GSHPx-1" }, { "synonym": "Cellular glutathione peroxidase" } ] }, "assessed_biomarker_entity_id": "UPKB:P07203", "assessed_entity_type": "protein", "specimen": [ { "name": "kidney", "id": "UBERON:0002113", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0002113", "loinc_code": "" } ], "evidence_source": [ { "id": "31844035", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31844035", "evidence_list": [ { "evidence": "Bioinformatics analysis found that high expression of GPX1 was positively correlated with tumor stage, distant metastasis and lymphatic metastasis. ROC curve analysis found that high expression of GPX1 could effectively distinguish ccRCC from normal individuals." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0002113" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:263", "recommended_name": { "id": "DOID:263", "name": "kidney cancer", "description": "A urinary system cancer that is located_in the kidney.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_263" }, "synonyms": [ { "id": "DOID:263", "name": "malignant tumour of kidney", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_263" }, { "id": "DOID:263", "name": "malignant neoplasm of kidney except pelvis", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_263" }, { "id": "DOID:263", "name": "renal cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_263" } ] }, "evidence_source": [ { "id": "31844035", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31844035", "evidence_list": [ { "evidence": "Bioinformatics analysis found that high expression of GPX1 was positively correlated with tumor stage, distant metastasis and lymphatic metastasis. ROC curve analysis found that high expression of GPX1 could effectively distinguish ccRCC from normal individuals." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "GPX1, a biomarker for the diagnosis and prognosis of kidney cancer, promotes the progression of kidney cancer.", "journal": "Aging", "authors": "Cheng Y, Xu T, Li S, Ruan H", "date": "2019-12-18", "evidence": [], "reference": [ { "id": "31844035", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31844035" } ] } ], "biomarker_canonical_id": "AN6701", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6702-1", "biomarker_component": [ { "biomarker": "increased SPAG9 level", "assessed_biomarker_entity": { "recommended_name": "C-Jun-amino-terminal kinase-interacting protein 4", "synonyms": [ { "synonym": "JIP-4" }, { "synonym": "JNK-interacting protein 4" }, { "synonym": "Cancer/testis antigen 89" }, { "synonym": "CT89" }, { "synonym": "Human lung cancer oncogene 6 protein" }, { "synonym": "HLC-6" }, { "synonym": "JNK-associated leucine-zipper protein" }, { "synonym": "JLP" }, { "synonym": "Mitogen-activated protein kinase 8-interacting protein 4" }, { "synonym": "Proliferation-inducing protein 6" }, { "synonym": "Protein highly expressed in testis" }, { "synonym": "PHET" }, { "synonym": "Sperm surface protein" }, { "synonym": "Sperm-associated antigen 9" }, { "synonym": "Sperm-specific protein" }, { "synonym": "Sunday driver 1" } ] }, "assessed_biomarker_entity_id": "UPKB:O60271", "assessed_entity_type": "protein", "specimen": [ { "name": "skin epidermis", "id": "UBERON:0001003", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0001003", "loinc_code": "" } ], "evidence_source": [ { "id": "25033008", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/25033008", "evidence_list": [ { "evidence": "SPAG9 was upregulated in NMSC when compared with normal skin. In conclusion, SPAG9 is expressed in NMSC cases." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0001003" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_4159" }, "synonyms": [ { "id": "DOID:4159", "name": "CA - skin cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_4159" }, { "id": "DOID:4159", "name": "malignant neoplasm of skin", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_4159" }, { "id": "DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_4159" } ] }, "evidence_source": [ { "id": "25033008", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/25033008", "evidence_list": [ { "evidence": "SPAG9 was upregulated in NMSC when compared with normal skin. In conclusion, SPAG9 is expressed in NMSC cases." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Immunohistochemical expression of sperm-associated antigen 9 in nonmelanoma skin cancer.", "journal": "The American Journal of dermatopathology", "authors": "Seleit I, Bakry OA, Samaka RM, Malak MA", "date": "2014-07-18", "evidence": [], "reference": [ { "id": "25033008", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/25033008" } ] } ], "biomarker_canonical_id": "AN6702", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6703-1", "biomarker_component": [ { "biomarker": "decreased FGFR3 level", "assessed_biomarker_entity": { "recommended_name": "Fibroblast growth factor receptor 3", "synonyms": [ { "synonym": "ACH" }, { "synonym": "CD333" }, { "synonym": "CEK2" }, { "synonym": "HSFGFR3EX" }, { "synonym": "JTK4" } ] }, "assessed_biomarker_entity_id": "NCBI: 2261", "assessed_entity_type": "gene", "specimen": [ { "name": "urinary bladder", "id": "UBERON:0001255", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0001255", "loinc_code": "" } ], "evidence_source": [ { "id": "28927152", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/28927152", "evidence_list": [ { "evidence": "Low FGFR3 expression level was associated with high-grade tumors and cancer progression (P=0.006 and P=0.001), whereas FGFR3 mutation status was not associated with cancer progression. Kaplan-Meier analysis revealed a similar result (log-rank, P<0.001). Multivariate analysis identified low FGFR3 expression level (odds ratio, 3.300; 95% confidence interval, 1.310-8.313; P=0.011) as an independent predictor of cancer progression." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0001255" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11054" }, "synonyms": [ { "id": "DOID:11054", "name": "tumor of the bladder", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11054" }, { "id": "DOID:11054", "name": "bladder cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11054" } ] }, "evidence_source": [ { "id": "28927152", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/28927152", "evidence_list": [ { "evidence": "Low FGFR3 expression level was associated with high-grade tumors and cancer progression (P=0.006 and P=0.001), whereas FGFR3 mutation status was not associated with cancer progression. Kaplan-Meier analysis revealed a similar result (log-rank, P<0.001). Multivariate analysis identified low FGFR3 expression level (odds ratio, 3.300; 95% confidence interval, 1.310-8.313; P=0.011) as an independent predictor of cancer progression." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Expression levels of ", "journal": "Oncology letters", "authors": "Kang HW, Kim YH, Jeong P, Park C, Kim WT, Ryu DH, Cha EJ, Ha YS, Kim TH, Kwon TG, Moon SK, Choi YH, Yun SJ, Kim WJ", "date": "2017-09-21", "evidence": [], "reference": [ { "id": "28927152", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/28927152" } ] } ], "biomarker_canonical_id": "AN6703", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "f": "frequency", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6704-1", "biomarker_component": [ { "biomarker": "increased methylation in BARHL2", "assessed_biomarker_entity": { "recommended_name": "BarH-like 2 homeobox protein gene", "synonyms": [] }, "assessed_biomarker_entity_id": "NCBI: 343472", "assessed_entity_type": "gene", "specimen": [ { "name": "stomach", "id": "UBERON:0000945", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000945", "loinc_code": "" } ], "evidence_source": [ { "id": "27441821", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/27441821", "evidence_list": [ { "evidence": "High levels of BARHL2 methylation were detected in three of seven GC cell lines; consistent with this, these cell lines expressed low levels of BARHL2. Treatment of these cell lines with 5-aza-2'-deoxycytidine restored BARHL2 expression. Levels of BARHL2 methylation in 18 normal and 14 atrophic gastritis samples were low irrespective of Helicobacter pylori infection. High levels of BARHL2 methylation were observed in gastric wash-derived DNA obtained from early GC patients before endoscopic resection (ER), but methylation was significantly lower after curative ER. Analysis using gastric juice derived exoDNA samples revealed that BARHL2 methylation yielded an area under the curve of 0.923 with 90% sensitivity and 100% specificity with respect to discriminating GC patients from non-GC controls." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000945" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" }, "synonyms": [ { "id": "DOID:10534", "name": "gastric neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" }, { "id": "DOID:10534", "name": "gastric cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" } ] }, "evidence_source": [ { "id": "27441821", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/27441821", "evidence_list": [ { "evidence": "High levels of BARHL2 methylation were detected in three of seven GC cell lines; consistent with this, these cell lines expressed low levels of BARHL2. Treatment of these cell lines with 5-aza-2'-deoxycytidine restored BARHL2 expression. Levels of BARHL2 methylation in 18 normal and 14 atrophic gastritis samples were low irrespective of Helicobacter pylori infection. High levels of BARHL2 methylation were observed in gastric wash-derived DNA obtained from early GC patients before endoscopic resection (ER), but methylation was significantly lower after curative ER. Analysis using gastric juice derived exoDNA samples revealed that BARHL2 methylation yielded an area under the curve of 0.923 with 90% sensitivity and 100% specificity with respect to discriminating GC patients from non-GC controls." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "BARHL2 Methylation Using Gastric Wash DNA or Gastric Juice Exosomal DNA is a Useful Marker For Early Detection of Gastric Cancer in an H. pylori-Independent Manner.", "journal": "Clinical and translational gastroenterology", "authors": "Yamamoto H, Watanabe Y, Oikawa R, Morita R, Yoshida Y, Maehata T, Yasuda H, Itoh F", "date": "2016-07-22", "evidence": [], "reference": [ { "id": "27441821", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/27441821" } ] } ], "biomarker_canonical_id": "AN6704", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "w": "weight", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6705-1", "biomarker_component": [ { "biomarker": "increased methylation in GFRA3", "assessed_biomarker_entity": { "recommended_name": "GDNF family receptor alpha-3 gene", "synonyms": [ { "synonym": "GDNFR3" } ] }, "assessed_biomarker_entity_id": "NCBI: 2676", "assessed_entity_type": "gene", "specimen": [ { "name": "stomach", "id": "UBERON:0000945", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000945", "loinc_code": "" } ], "evidence_source": [ { "id": "26984265", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/26984265", "evidence_list": [ { "evidence": "The different DNA methylation clusters of the tumors and normal tissue indicate that aberrant DNA methylation is a distinct feature of gastric cancer, although there is little difference in the overall, and low, methylation levels between the two tissue types. The GFRA3 promoter region showed marked hypermethylation in almost all tumors, and its correlation with survival and other clinicopathological parameters may have important prognostic significance." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000945" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" }, "synonyms": [ { "id": "DOID:10534", "name": "gastric neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" }, { "id": "DOID:10534", "name": "gastric cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" } ] }, "evidence_source": [ { "id": "26984265", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/26984265", "evidence_list": [ { "evidence": "The different DNA methylation clusters of the tumors and normal tissue indicate that aberrant DNA methylation is a distinct feature of gastric cancer, although there is little difference in the overall, and low, methylation levels between the two tissue types. The GFRA3 promoter region showed marked hypermethylation in almost all tumors, and its correlation with survival and other clinicopathological parameters may have important prognostic significance." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "GFRA3 promoter methylation may be associated with decreased postoperative survival in gastric cancer.", "journal": "BMC cancer", "authors": "Eftang LL, Klajic J, Kristensen VN, Tost J, Esbensen QY, Blom GP, Bukholm IR, Bukholm G", "date": "2016-03-18", "evidence": [], "reference": [ { "id": "26984265", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/26984265" } ] } ], "biomarker_canonical_id": "AN6705", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "f": "frequency", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6706-1", "biomarker_component": [ { "biomarker": "decreased GPX3 level", "assessed_biomarker_entity": { "recommended_name": "Glutathione peroxidase 3", "synonyms": [ { "synonym": "GPx-P" }, { "synonym": "GSHPx-3" }, { "synonym": "GSHPx-P" } ] }, "assessed_biomarker_entity_id": "NCBI: 2878", "assessed_entity_type": "gene", "specimen": [ { "name": "stomach", "id": "UBERON:0000945", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000945", "loinc_code": "" } ], "evidence_source": [ { "id": "23071548", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/23071548", "evidence_list": [ { "evidence": "Downregulation or silencing of GPX3 was detected in 8 of 9 cancer cell lines, 83% (90/108) gastric cancers samples, as compared to non-tumor adjacent normal gastric samples (P<0.0001). Examination of GPX3 promoter demonstrated DNA hypermethylation (= 10% methylation level determined by Bisulfite Pyrosequencing) in 6 of 9 cancer cell lines and 60% of gastric cancer samples (P = 0.007). We also detected a significant loss of DNA copy number of GPX3 in gastric cancers (P<0.001)." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000945" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" }, "synonyms": [ { "id": "DOID:10534", "name": "gastric neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" }, { "id": "DOID:10534", "name": "gastric cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10534" } ] }, "evidence_source": [ { "id": "23071548", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/23071548", "evidence_list": [ { "evidence": "Downregulation or silencing of GPX3 was detected in 8 of 9 cancer cell lines, 83% (90/108) gastric cancers samples, as compared to non-tumor adjacent normal gastric samples (P<0.0001). Examination of GPX3 promoter demonstrated DNA hypermethylation (= 10% methylation level determined by Bisulfite Pyrosequencing) in 6 of 9 cancer cell lines and 60% of gastric cancer samples (P = 0.007). We also detected a significant loss of DNA copy number of GPX3 in gastric cancers (P<0.001)." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Silencing of glutathione peroxidase 3 through DNA hypermethylation is associated with lymph node metastasis in gastric carcinomas.", "journal": "PloS one", "authors": "Peng DF, Hu TL, Schneider BG, Chen Z, Xu ZK, El-Rifai W", "date": "2012-10-17", "evidence": [], "reference": [ { "id": "23071548", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/23071548" } ] } ], "biomarker_canonical_id": "AN6706", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6707-1", "biomarker_component": [ { "biomarker": "increased SNHG5 level", "assessed_biomarker_entity": { "recommended_name": "Long noncoding RNA SNHG5", "synonyms": [] }, "assessed_biomarker_entity_id": "RNAC:URS000075B42D", "assessed_entity_type": "RNA", "specimen": [ { "name": "kidney", "id": "UBERON:0002113", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0002113", "loinc_code": "" } ], "evidence_source": [ { "id": "32281285", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32281285", "evidence_list": [ { "evidence": "SNHG5 expression was found to be remarkably increased in ccRCC samples." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0002113" } ] }, { "id": "32194916", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32194916", "evidence_list": [ { "evidence": "SNHG5 expression levels were significantly increased in ccRCC tissues compared to those in non-tumor tissue. Inhibition of SNHG5 expression significantly reduced invasion ability and increased apoptosis rate of 786-O RCC cells infected with shR-NA-SNHG5." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0002113" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:263", "recommended_name": { "id": "DOID:263", "name": "kidney cancer", "description": "A urinary system cancer that is located_in the kidney.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_263" }, "synonyms": [ { "id": "DOID:263", "name": "malignant tumour of kidney", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_263" }, { "id": "DOID:263", "name": "malignant neoplasm of kidney except pelvis", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_263" }, { "id": "DOID:263", "name": "renal cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_263" } ] }, "evidence_source": [ { "id": "32281285", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32281285", "evidence_list": [ { "evidence": "SNHG5 expression was found to be remarkably increased in ccRCC samples." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "32194916", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32194916", "evidence_list": [ { "evidence": "SNHG5 expression levels were significantly increased in ccRCC tissues compared to those in non-tumor tissue. Inhibition of SNHG5 expression significantly reduced invasion ability and increased apoptosis rate of 786-O RCC cells infected with shR-NA-SNHG5." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "The lncRNA SNHG5-mediated miR-205-5p downregulation contributes to the progression of clear cell renal cell carcinoma by targeting ZEB1.", "journal": "Cancer medicine", "authors": "Xiang W, Lv L, Zhou G, Wu W, Yuan J, Zhang C, Jiang G", "date": "2020-04-14", "evidence": [], "reference": [ { "id": "32281285", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32281285" } ] }, { "title": "Long non-coding RNA SNHG5 affects the invasion and apoptosis of renal cell carcinoma by regulating the miR-363-3p-Twist1 interaction.", "journal": "American journal of translational research", "authors": "Li WZ, Zou Y, Song ZY, Wei ZW, Chen G, Cai QL, Wang Z", "date": "2020-03-21", "evidence": [], "reference": [ { "id": "32194916", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/32194916" } ] } ], "biomarker_canonical_id": "AN6707", "score": 1.2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 1 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "f": "frequency", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6708-1", "biomarker_component": [ { "biomarker": "increased antigen level", "assessed_biomarker_entity": { "recommended_name": "Sialylated tumor-related antigen", "synonyms": [] }, "assessed_biomarker_entity_id": "GTC:G78959US", "assessed_entity_type": "glycan", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "33093149", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/33093149", "evidence_list": [ { "evidence": "Furthermore, a blood-plasma test for the sTRA glycan identified the PDACs that showed rapid relapse following neoadjuvant chemotherapy. This research demonstrates the use of the sTRA glycan to identify the PDAC cases that are highly resistant to chemotherapy." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "predictive" } ], "condition": { "id": "DOID:1793", "recommended_name": { "id": "DOID:1793", "name": "pancreatic cancer", "description": "An endocrine gland cancer located_in the pancreas.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, "synonyms": [ { "id": "DOID:1793", "name": "Ca head of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "Ca body of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "pancreatic tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "malignant neoplasm of tail of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "malignant neoplasm of head of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "pancreatic neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "Ca tail of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "pancreas neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" }, { "id": "DOID:1793", "name": "malignant neoplasm of body of pancreas", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1793" } ] }, "evidence_source": [ { "id": "33093149", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/33093149", "evidence_list": [ { "evidence": "Furthermore, a blood-plasma test for the sTRA glycan identified the PDACs that showed rapid relapse following neoadjuvant chemotherapy. This research demonstrates the use of the sTRA glycan to identify the PDAC cases that are highly resistant to chemotherapy." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Detection of Chemotherapy-resistant Pancreatic Cancer Using a Glycan Biomarker, sTRA.", "journal": "Clinical cancer research : an official journal of the American Association for Cancer Research", "authors": "Gao C, Wisniewski L, Liu Y, Staal B, Beddows I, Plenker D, Aldakkak M, Hall J, Barnett D, Gouda MK, Allen P, Drake R, Zureikat A, Huang Y, Evans D, Singhi A, Brand RE, Tuveson DA, Tsai S, Haab BB", "date": "2020-10-24", "evidence": [], "reference": [ { "id": "33093149", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/33093149" } ] } ], "biomarker_canonical_id": "AN6708", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "c": "condition", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6709-1", "biomarker_component": [ { "biomarker": "increased N-glycan level", "assessed_biomarker_entity": { "recommended_name": "Lewis x fucosylated monogalactosylated triantennary N-glycan", "synonyms": [] }, "assessed_biomarker_entity_id": "GTC:G36521AS", "assessed_entity_type": "glycan", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "18818422", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/18818422", "evidence_list": [ { "evidence": "Following digestion with sialidase and beta-galactosidase, the alpha1,3-fucosylated trisialylated triantennary structure (A3FG3S3, GU 10.75) digested to form the alpha1,3-fucosylated monogalactosylated triantennary structure (A3FG1). We observed a significant difference in the trends of both A3FG1 and CA 15-3 in all 10 patients. Interestingly, we found that A3FG1 increased in all the second samples, clearly consistent with breast cancer progression and/or metastasis. This preliminary result suggests that compared to the commonly measured CA 15-3 and CEA, the glycan marker A3FG1, quantified from whole serum of breast cancer patients, could be more reliable for detecting disease progression and metastasis." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "name": "breast cancer", "description": "A thoracic cancer that originates in the mammary gland.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, "synonyms": [ { "id": "DOID:1612", "name": "malignant tumor of the breast", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "breast tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "mammary cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "primary breast cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "mammary tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "malignant neoplasm of breast", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" } ] }, "evidence_source": [ { "id": "18818422", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/18818422", "evidence_list": [ { "evidence": "Following digestion with sialidase and beta-galactosidase, the alpha1,3-fucosylated trisialylated triantennary structure (A3FG3S3, GU 10.75) digested to form the alpha1,3-fucosylated monogalactosylated triantennary structure (A3FG1). We observed a significant difference in the trends of both A3FG1 and CA 15-3 in all 10 patients. Interestingly, we found that A3FG1 increased in all the second samples, clearly consistent with breast cancer progression and/or metastasis. This preliminary result suggests that compared to the commonly measured CA 15-3 and CEA, the glycan marker A3FG1, quantified from whole serum of breast cancer patients, could be more reliable for detecting disease progression and metastasis." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "A strategy to reveal potential glycan markers from serum glycoproteins associated with breast cancer progression.", "journal": "Glycobiology", "authors": "Abd Hamid UM, Royle L, Saldova R, Radcliffe CM, Harvey DJ, Storr SJ, Pardo M, Antrobus R, Chapman CJ, Zitzmann N, Robertson JF, Dwek RA, Rudd PM", "date": "2008-09-27", "evidence": [], "reference": [ { "id": "18818422", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/18818422" } ] } ], "biomarker_canonical_id": "AN6709", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "c": "condition", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6710-1", "biomarker_component": [ { "biomarker": "decreased FTO level", "assessed_biomarker_entity": { "recommended_name": "Alpha-ketoglutarate-dependent dioxygenase FTO", "synonyms": [ { "synonym": "Fat mass and obesity-associated protein" }, { "synonym": "U6 small nuclear RNA (2'-O-methyladenosine-N(6)-)-demethylase FTO" }, { "synonym": "U6 small nuclear RNA N(6)-methyladenosine-demethylase FTO" }, { "synonym": "mRNA (2'-O-methyladenosine-N(6)-)-demethylase FTO" }, { "synonym": "m6A(m)-demethylase FTO" }, { "synonym": "mRNA N(6)-methyladenosine demethylase FTO" }, { "synonym": "tRNA N1-methyl adenine demethylase FTO" } ] }, "assessed_biomarker_entity_id": "UPKB:Q9C0B1", "assessed_entity_type": "protein", "specimen": [ { "name": "kidney", "id": "UBERON:0002113", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0002113", "loinc_code": "" } ], "evidence_source": [ { "id": "31985880", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31985880", "evidence_list": [ { "evidence": "ALKBH5 was significantly reduced in RCC compared to normal tissue (P < 0.001), low expression levels of ALKBH5 and FTO were correlated with a shorter overall survival (OS: ALKBH5 log-rank P = 0.007; FTO log-rank P = 0.033) and cancer-specific survival (CSS: ALKBH5 log-rank P = 0.018; FTO log-rank P = 0.029" } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0002113" } ] }, { "id": "34683137", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/34683137", "evidence_list": [ { "evidence": "ALKBH5 was significantly reduced in RCC compared to normal tissue (P < 0.001), low expression levels of ALKBH5 and FTO were correlated with a shorter overall survival (OS: ALKBH5 log-rank P = 0.007; FTO log-rank P = 0.033) and cancer-specific survival (CSS: ALKBH5 log-rank P = 0.018; FTO log-rank P = 0.029 [PMID: 31985880]. Univariate analysis showed that higher FTO expression was associated with better overall and progression free survival in both ccRCC and pRCC patients. No associations were disclosed concerning ALKBH5 expressions levels." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0002113" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:263", "recommended_name": { "id": "DOID:263", "name": "kidney cancer", "description": "A urinary system cancer that is located_in the kidney.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_263" }, "synonyms": [ { "id": "DOID:263", "name": "malignant tumour of kidney", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_263" }, { "id": "DOID:263", "name": "malignant neoplasm of kidney except pelvis", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_263" }, { "id": "DOID:263", "name": "renal cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_263" } ] }, "evidence_source": [ { "id": "31985880", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31985880", "evidence_list": [ { "evidence": "ALKBH5 was significantly reduced in RCC compared to normal tissue (P < 0.001), low expression levels of ALKBH5 and FTO were correlated with a shorter overall survival (OS: ALKBH5 log-rank P = 0.007; FTO log-rank P = 0.033) and cancer-specific survival (CSS: ALKBH5 log-rank P = 0.018; FTO log-rank P = 0.029" } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "34683137", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/34683137", "evidence_list": [ { "evidence": "ALKBH5 was significantly reduced in RCC compared to normal tissue (P < 0.001), low expression levels of ALKBH5 and FTO were correlated with a shorter overall survival (OS: ALKBH5 log-rank P = 0.007; FTO log-rank P = 0.033) and cancer-specific survival (CSS: ALKBH5 log-rank P = 0.018; FTO log-rank P = 0.029 [PMID: 31985880]. Univariate analysis showed that higher FTO expression was associated with better overall and progression free survival in both ccRCC and pRCC patients. No associations were disclosed concerning ALKBH5 expressions levels." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "The N", "journal": "BJU international", "authors": "Strick A, von Hagen F, Gundert L, Klümper N, Tolkach Y, Schmidt D, Kristiansen G, Toma M, Ritter M, Ellinger J", "date": "2020-01-28", "evidence": [], "reference": [ { "id": "31985880", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31985880" } ] }, { "title": "Deregulation of N6-Methyladenosine RNA Modification and Its Erasers FTO/ALKBH5 among the Main Renal Cell Tumor Subtypes.", "journal": "Journal of personalized medicine", "authors": "Guimarães-Teixeira C, Barros-Silva D, Lobo J, Soares-Fernandes D, Constâncio V, Leite-Silva P, Silva-Santos R, Braga I, Henrique R, Miranda-Gonçalves V, Jerónimo C", "date": "2021-10-24", "evidence": [], "reference": [ { "id": "34683137", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/34683137" } ] } ], "biomarker_canonical_id": "AN6710", "score": 1.2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 1 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6711-1", "biomarker_component": [ { "biomarker": "decreased ALKBH5 level", "assessed_biomarker_entity": { "recommended_name": "Alkylation repair homologue 5", "synonyms": [ { "synonym": "Alkylated DNA repair protein alkB homolog 5" }, { "synonym": "Alpha-ketoglutarate-dependent dioxygenase alkB homolog 5" } ] }, "assessed_biomarker_entity_id": "UPKB:Q6P6C2", "assessed_entity_type": "protein", "specimen": [ { "name": "kidney", "id": "UBERON:0002113", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0002113", "loinc_code": "" } ], "evidence_source": [ { "id": "31985880", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31985880", "evidence_list": [ { "evidence": "ALKBH5 was significantly reduced in RCC compared to normal tissue (P < 0.001), low expression levels of ALKBH5 and FTO were correlated with a shorter overall survival (OS: ALKBH5 log-rank P = 0.007; FTO log-rank P = 0.033) and cancer-specific survival (CSS: ALKBH5 log-rank P = 0.018; FTO log-rank P = 0.029" } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0002113" } ] }, { "id": "34683137", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/34683137", "evidence_list": [ { "evidence": ". Univariate analysis showed that higher FTO expression was associated with better overall and progression free survival in both ccRCC and pRCC patients. No associations were disclosed concerning ALKBH5 expressions levels." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0002113" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:263", "recommended_name": { "id": "DOID:263", "name": "kidney cancer", "description": "A urinary system cancer that is located_in the kidney.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_263" }, "synonyms": [ { "id": "DOID:263", "name": "malignant tumour of kidney", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_263" }, { "id": "DOID:263", "name": "malignant neoplasm of kidney except pelvis", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_263" }, { "id": "DOID:263", "name": "renal cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_263" } ] }, "evidence_source": [ { "id": "31985880", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31985880", "evidence_list": [ { "evidence": "ALKBH5 was significantly reduced in RCC compared to normal tissue (P < 0.001), low expression levels of ALKBH5 and FTO were correlated with a shorter overall survival (OS: ALKBH5 log-rank P = 0.007; FTO log-rank P = 0.033) and cancer-specific survival (CSS: ALKBH5 log-rank P = 0.018; FTO log-rank P = 0.029" } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] }, { "id": "34683137", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/34683137", "evidence_list": [ { "evidence": ". Univariate analysis showed that higher FTO expression was associated with better overall and progression free survival in both ccRCC and pRCC patients. No associations were disclosed concerning ALKBH5 expressions levels." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "The N", "journal": "BJU international", "authors": "Strick A, von Hagen F, Gundert L, Klümper N, Tolkach Y, Schmidt D, Kristiansen G, Toma M, Ritter M, Ellinger J", "date": "2020-01-28", "evidence": [], "reference": [ { "id": "31985880", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31985880" } ] }, { "title": "Deregulation of N6-Methyladenosine RNA Modification and Its Erasers FTO/ALKBH5 among the Main Renal Cell Tumor Subtypes.", "journal": "Journal of personalized medicine", "authors": "Guimarães-Teixeira C, Barros-Silva D, Lobo J, Soares-Fernandes D, Constâncio V, Leite-Silva P, Silva-Santos R, Braga I, Henrique R, Miranda-Gonçalves V, Jerónimo C", "date": "2021-10-24", "evidence": [], "reference": [ { "id": "34683137", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/34683137" } ] } ], "biomarker_canonical_id": "AN6711", "score": 1.2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 1 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6712-1", "biomarker_component": [ { "biomarker": "differentially measured MIR-576 level", "assessed_biomarker_entity": { "recommended_name": "miR-576", "synonyms": [] }, "assessed_biomarker_entity_id": "MRB:MI0003583", "assessed_entity_type": "RNA", "specimen": [ { "name": "kidney", "id": "UBERON:0002113", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0002113", "loinc_code": "" } ], "evidence_source": [ { "id": "31350524", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31350524", "evidence_list": [ { "evidence": "Thirteen miRNAs that were significantly differentially expressed in RCC patients were identified, 10 of them have been proved to be associated with kidney cancer in other studies, miR-576, miR-616 and miR-133a-2 are three newly discovered biomarkers of RCC in this study. We found that the target genes of miR-576 (CUL3 and RAC1) are involved in the regulation of multiple cancer-related biological pathways, and the target gene of miR-616 (ASB13 and FBXW2) has been reported to be associated with the development of other cancers. Our findings may have guiding significance for the early diagnosis of renal cell carcinoma." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0002113" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:263", "recommended_name": { "id": "DOID:263", "name": "kidney cancer", "description": "A urinary system cancer that is located_in the kidney.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_263" }, "synonyms": [ { "id": "DOID:263", "name": "malignant tumour of kidney", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_263" }, { "id": "DOID:263", "name": "malignant neoplasm of kidney except pelvis", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_263" }, { "id": "DOID:263", "name": "renal cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_263" } ] }, "evidence_source": [ { "id": "31350524", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31350524", "evidence_list": [ { "evidence": "Thirteen miRNAs that were significantly differentially expressed in RCC patients were identified, 10 of them have been proved to be associated with kidney cancer in other studies, miR-576, miR-616 and miR-133a-2 are three newly discovered biomarkers of RCC in this study. We found that the target genes of miR-576 (CUL3 and RAC1) are involved in the regulation of multiple cancer-related biological pathways, and the target gene of miR-616 (ASB13 and FBXW2) has been reported to be associated with the development of other cancers. Our findings may have guiding significance for the early diagnosis of renal cell carcinoma." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Computational identification and analysis of early diagnostic biomarkers for kidney cancer.", "journal": "Journal of human genetics", "authors": "Tang T, Du X, Zhang X, Niu W, Li C, Tan J", "date": "2019-07-28", "evidence": [], "reference": [ { "id": "31350524", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31350524" } ] } ], "biomarker_canonical_id": "AN6712", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "f": "frequency", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6713-1", "biomarker_component": [ { "biomarker": "differentially measured MIR-616 level", "assessed_biomarker_entity": { "recommended_name": "miR-616", "synonyms": [] }, "assessed_biomarker_entity_id": "MRB:MI0003629", "assessed_entity_type": "RNA", "specimen": [ { "name": "kidney", "id": "UBERON:0002113", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0002113", "loinc_code": "" } ], "evidence_source": [ { "id": "31350524", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31350524", "evidence_list": [ { "evidence": "Thirteen miRNAs that were significantly differentially expressed in RCC patients were identified, 10 of them have been proved to be associated with kidney cancer in other studies, miR-576, miR-616 and miR-133a-2 are three newly discovered biomarkers of RCC in this study. We found that the target genes of miR-576 (CUL3 and RAC1) are involved in the regulation of multiple cancer-related biological pathways, and the target gene of miR-616 (ASB13 and FBXW2) has been reported to be associated with the development of other cancers. Our findings may have guiding significance for the early diagnosis of renal cell carcinoma." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0002113" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:263", "recommended_name": { "id": "DOID:263", "name": "kidney cancer", "description": "A urinary system cancer that is located_in the kidney.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_263" }, "synonyms": [ { "id": "DOID:263", "name": "malignant tumour of kidney", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_263" }, { "id": "DOID:263", "name": "malignant neoplasm of kidney except pelvis", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_263" }, { "id": "DOID:263", "name": "renal cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_263" } ] }, "evidence_source": [ { "id": "31350524", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31350524", "evidence_list": [ { "evidence": "Thirteen miRNAs that were significantly differentially expressed in RCC patients were identified, 10 of them have been proved to be associated with kidney cancer in other studies, miR-576, miR-616 and miR-133a-2 are three newly discovered biomarkers of RCC in this study. We found that the target genes of miR-576 (CUL3 and RAC1) are involved in the regulation of multiple cancer-related biological pathways, and the target gene of miR-616 (ASB13 and FBXW2) has been reported to be associated with the development of other cancers. Our findings may have guiding significance for the early diagnosis of renal cell carcinoma." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Computational identification and analysis of early diagnostic biomarkers for kidney cancer.", "journal": "Journal of human genetics", "authors": "Tang T, Du X, Zhang X, Niu W, Li C, Tan J", "date": "2019-07-28", "evidence": [], "reference": [ { "id": "31350524", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31350524" } ] } ], "biomarker_canonical_id": "AN6713", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "c": "condition", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6714-1", "biomarker_component": [ { "biomarker": "increased P4HB level", "assessed_biomarker_entity": { "recommended_name": "Prolyl 4-hydroxylase, beta polypeptide", "synonyms": [ { "synonym": "PDI" }, { "synonym": "Cellular thyroid hormone-binding protein" }, { "synonym": "Prolyl 4-hydroxylase subunit beta" }, { "synonym": "p55" } ] }, "assessed_biomarker_entity_id": "UPKB:P07237", "assessed_entity_type": "protein", "specimen": [ { "name": "kidney", "id": "UBERON:0002113", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0002113", "loinc_code": "" } ], "evidence_source": [ { "id": "31350524", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31350524", "evidence_list": [ { "evidence": "High expression of P4HB mRNA was related to significantly worse Overall Survival (OS) for KIRC patients (Kidney renal cell carcinoma) (p<0.0001). Univariate Cox regression analyses, showed higher stage and high P4HB mRNA expression exhibited unfavorable effects on OS (p<0.0001 and p<0.0001)." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0002113" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:263", "recommended_name": { "id": "DOID:263", "name": "kidney cancer", "description": "A urinary system cancer that is located_in the kidney.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_263" }, "synonyms": [ { "id": "DOID:263", "name": "malignant tumour of kidney", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_263" }, { "id": "DOID:263", "name": "malignant neoplasm of kidney except pelvis", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_263" }, { "id": "DOID:263", "name": "renal cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_263" } ] }, "evidence_source": [ { "id": "31350524", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/31350524", "evidence_list": [ { "evidence": "High expression of P4HB mRNA was related to significantly worse Overall Survival (OS) for KIRC patients (Kidney renal cell carcinoma) (p<0.0001). 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The combination of markers yielded an AUC of 0.86, 0.85 and 0.88 for OSCC total, T1-T2, and T3-T4, respectively." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Oral squamous cell carcinoma detection by salivary biomarkers in a Serbian population.", "journal": "Oral oncology", "authors": "Brinkmann O, Kastratovic DA, Dimitrijevic MV, Konstantinovic VS, Jelovac DB, Antic J, Nesic VS, Markovic SZ, Martinovic ZR, Akin D, Spielmann N, Zhou H, Wong DT", "date": "2010-11-27", "evidence": [], "reference": [ { "id": "21109482", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/21109482" } ] } ], "biomarker_canonical_id": "AN6782", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "c": "condition", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6783-1", "biomarker_component": [ { "biomarker": "increased SAT1 level", "assessed_biomarker_entity": { "recommended_name": "Diamine acetyltransferase 1", "synonyms": [ { "synonym": "Polyamine N-acetyltransferase 1" }, { "synonym": "Putrescine acetyltransferase" }, { "synonym": "Spermidine/spermine N(1)-acetyltransferase 1" }, { "synonym": "SSAT" }, { "synonym": "SSAT-1" } ] }, "assessed_biomarker_entity_id": "UPKB:P21673", "assessed_entity_type": "protein", "specimen": [ { "name": "saliva", "id": "UBERON:0001836", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0001836", "loinc_code": "13629-1" } ], "evidence_source": [ { "id": "21109482", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/21109482", "evidence_list": [ { "evidence": "Four transcriptome (IL8, IL1B, SAT1, and S100P) and all proteome biomarkers were significantly elevated (p<0.05) in OSCC patients. The combination of markers yielded an AUC of 0.86, 0.85 and 0.88 for OSCC total, T1-T2, and T3-T4, respectively." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0001836" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:11934", "recommended_name": { "id": "DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11934" }, "synonyms": [ { "id": "DOID:11934", "name": "head and neck neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11934" }, { "id": "DOID:11934", "name": "head/neck neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11934" }, { "id": "DOID:11934", "name": "head and neck tumours", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11934" }, { "id": "DOID:11934", "name": "tumor of head and neck", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11934" } ] }, "evidence_source": [ { "id": "21109482", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/21109482", "evidence_list": [ { "evidence": "Four transcriptome (IL8, IL1B, SAT1, and S100P) and all proteome biomarkers were significantly elevated (p<0.05) in OSCC patients. The combination of markers yielded an AUC of 0.86, 0.85 and 0.88 for OSCC total, T1-T2, and T3-T4, respectively." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Oral squamous cell carcinoma detection by salivary biomarkers in a Serbian population.", "journal": "Oral oncology", "authors": "Brinkmann O, Kastratovic DA, Dimitrijevic MV, Konstantinovic VS, Jelovac DB, Antic J, Nesic VS, Markovic SZ, Martinovic ZR, Akin D, Spielmann N, Zhou H, Wong DT", "date": "2010-11-27", "evidence": [], "reference": [ { "id": "21109482", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/21109482" } ] } ], "biomarker_canonical_id": "AN6783", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "c": "condition", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6372-6", "biomarker_component": [ { "biomarker": "increased IL8 level", "assessed_biomarker_entity": { "recommended_name": "Interleukin-8", "synonyms": [ { "synonym": "IL-8" }, { "synonym": "C-X-C motif chemokine 8" }, { "synonym": "Chemokine (C-X-C motif) ligand 8" }, { "synonym": "Emoctakin" }, { "synonym": "Granulocyte chemotactic protein 1" }, { "synonym": "GCP-1" }, { "synonym": "Monocyte-derived neutrophil chemotactic factor" }, { "synonym": "MDNCF" }, { "synonym": "Monocyte-derived neutrophil-activating peptide" }, { "synonym": "MONAP" }, { "synonym": "Neutrophil-activating protein 1" }, { "synonym": "NAP-1" }, { "synonym": "Protein 3-10C" }, { "synonym": "T-cell chemotactic factor" } ] }, "assessed_biomarker_entity_id": "UPKB:P10145", "assessed_entity_type": "protein", "specimen": [ { "name": "saliva", "id": "UBERON:0001836", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0001836", "loinc_code": "" } ], "evidence_source": [ { "id": "21109482", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/21109482", "evidence_list": [ { "evidence": "Four transcriptome (IL8, IL1B, SAT1, and S100P) and all proteome biomarkers were significantly elevated (p<0.05) in OSCC patients. The combination of markers yielded an AUC of 0.86, 0.85 and 0.88 for OSCC total, T1-T2, and T3-T4, respectively." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0001836" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:11934", "recommended_name": { "id": "DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11934" }, "synonyms": [ { "id": "DOID:11934", "name": "head and neck neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11934" }, { "id": "DOID:11934", "name": "head/neck neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11934" }, { "id": "DOID:11934", "name": "head and neck tumours", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11934" }, { "id": "DOID:11934", "name": "tumor of head and neck", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11934" } ] }, "evidence_source": [ { "id": "21109482", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/21109482", "evidence_list": [ { "evidence": "Four transcriptome (IL8, IL1B, SAT1, and S100P) and all proteome biomarkers were significantly elevated (p<0.05) in OSCC patients. The combination of markers yielded an AUC of 0.86, 0.85 and 0.88 for OSCC total, T1-T2, and T3-T4, respectively." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Oral squamous cell carcinoma detection by salivary biomarkers in a Serbian population.", "journal": "Oral oncology", "authors": "Brinkmann O, Kastratovic DA, Dimitrijevic MV, Konstantinovic VS, Jelovac DB, Antic J, Nesic VS, Markovic SZ, Martinovic ZR, Akin D, Spielmann N, Zhou H, Wong DT", "date": "2010-11-27", "evidence": [], "reference": [ { "id": "21109482", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/21109482" } ] } ], "biomarker_canonical_id": "AN6372", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "f": "frequency", "c": "condition" } }, "collision": 0 }, { "biomarker_id": "AN6718-2", "biomarker_component": [ { "biomarker": "increased IL1B level", "assessed_biomarker_entity": { "recommended_name": "Interleukin-1 beta protein", "synonyms": [ { "synonym": "IL-1 beta" }, { "synonym": "Catabolin" } ] }, "assessed_biomarker_entity_id": "UPKB:P01584", "assessed_entity_type": "protein", "specimen": [ { "name": "saliva", "id": "UBERON:0001836", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0001836", "loinc_code": "13629-1" } ], "evidence_source": [ { "id": "21109482", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/21109482", "evidence_list": [ { "evidence": "IL1B protein and IL8 protein as well as S100P mRNA were increased the most between all OSCC patients and controls with a fold change of 3.96, 3.09, and 3.24 respectively. Combined markers proved to be the strongest discriminator of OSCC with an AUC of 0.86 for all cancer patients (IL1B protein + SAT1 mRNA + DUSP1 mRNA), 0.85 for T1-T2 (IL1B mRNA + SAT1 mRNA + DUSP1 mRNA), and 0.88 for T3-T4 (IL1B protein + DUSP1 mRNA) (Figure 1¬†and¬†Table 3). The sensitivity/specificity for these groups were 0.89/0.78, 0.67/0.96, and 0.82/0.84 respectively." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0001836" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:11934", "recommended_name": { "id": "DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11934" }, "synonyms": [ { "id": "DOID:11934", "name": "head and neck neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11934" }, { "id": "DOID:11934", "name": "head/neck neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11934" }, { "id": "DOID:11934", "name": "head and neck tumours", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11934" }, { "id": "DOID:11934", "name": "tumor of head and neck", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_11934" } ] }, "evidence_source": [ { "id": "21109482", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/21109482", "evidence_list": [ { "evidence": "IL1B protein and IL8 protein as well as S100P mRNA were increased the most between all OSCC patients and controls with a fold change of 3.96, 3.09, and 3.24 respectively. Combined markers proved to be the strongest discriminator of OSCC with an AUC of 0.86 for all cancer patients (IL1B protein + SAT1 mRNA + DUSP1 mRNA), 0.85 for T1-T2 (IL1B mRNA + SAT1 mRNA + DUSP1 mRNA), and 0.88 for T3-T4 (IL1B protein + DUSP1 mRNA) (Figure 1¬†and¬†Table 3). The sensitivity/specificity for these groups were 0.89/0.78, 0.67/0.96, and 0.82/0.84 respectively." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Oral squamous cell carcinoma detection by salivary biomarkers in a Serbian population.", "journal": "Oral oncology", "authors": "Brinkmann O, Kastratovic DA, Dimitrijevic MV, Konstantinovic VS, Jelovac DB, Antic J, Nesic VS, Markovic SZ, Martinovic ZR, Akin D, Spielmann N, Zhou H, Wong DT", "date": "2010-11-27", "evidence": [], "reference": [ { "id": "21109482", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/21109482" } ] } ], "biomarker_canonical_id": "AN6718", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "f": "frequency", "c": "condition", "w": "weight" } }, "collision": 0 }, { "biomarker_id": "AN6721-1", "biomarker_component": [ { "biomarker": "decreased IL1B level", "assessed_biomarker_entity": { "recommended_name": "Interleukin-1 beta protein", "synonyms": [ { "synonym": "IL-1" }, { "synonym": "IL1-BETA" }, { "synonym": "IL1F2" }, { "synonym": "IL1beta" } ] }, "assessed_biomarker_entity_id": "NCBI: 3553", "assessed_entity_type": "gene", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "13629-1" } ], "evidence_source": [ { "id": "17595242", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/17595242", "evidence_list": [ { "evidence": "Changes in expression of IL1B, early growth response gene 3, and prostaglandin-endoperoxide synthase 2 resolved within 4 months of insulin therapy and were also observed in T2D, suggesting that they resulted from hyperglycemia. With use of a knowledge base, 81 of 282 genes could be placed within a network of interrelated genes with predicted functions including apoptosis and cell proliferation. IL1B and the MYC oncogene were the most highly connected genes in the network. IL1B was highly overexpressed in both T1D and T2D, whereas MYC was dysregulated only in T1D." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "monitoring" } ], "condition": { "id": "DOID:9351", "recommended_name": { "id": "DOID:9351", "name": "diabetes mellitus", "description": "A glucose metabolism disease that is characterized by chronic hyperglycaemia with disturbances of carbohydrate, fat and protein metabolism resulting from defects in insulin secretion, insulin action, or both.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_9351" }, "synonyms": [ { "id": "DOID:9351", "name": "diabetes", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_9351" } ] }, "evidence_source": [ { "id": "17595242", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/17595242", "evidence_list": [ { "evidence": "Changes in expression of IL1B, early growth response gene 3, and prostaglandin-endoperoxide synthase 2 resolved within 4 months of insulin therapy and were also observed in T2D, suggesting that they resulted from hyperglycemia. With use of a knowledge base, 81 of 282 genes could be placed within a network of interrelated genes with predicted functions including apoptosis and cell proliferation. IL1B and the MYC oncogene were the most highly connected genes in the network. IL1B was highly overexpressed in both T1D and T2D, whereas MYC was dysregulated only in T1D." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Gene expression in peripheral blood mononuclear cells from children with diabetes.", "journal": "The Journal of clinical endocrinology and metabolism", "authors": "Kaizer EC, Glaser CL, Chaussabel D, Banchereau J, Pascual V, White PC", "date": "2007-06-28", "evidence": [], "reference": [ { "id": "17595242", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/17595242" } ] } ], "biomarker_canonical_id": "AN6721", "score": 2, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 1 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6722-1", "biomarker_component": [ { "biomarker": "methylation in RASSF1", "assessed_biomarker_entity": { "recommended_name": "Ras association domain-containing protein 1 gene", "synonyms": [ { "synonym": "123F2" }, { "synonym": "NORE2A" }, { "synonym": "RASSF1A" }, { "synonym": "RDA32" }, { "synonym": "REH3P21" } ] }, "assessed_biomarker_entity_id": "NCBI: 11186", "assessed_entity_type": "gene", "specimen": [ { "name": "urine", "id": "UBERON:0001088", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0001088", "loinc_code": "" } ], "evidence_source": [ { "id": "24980613", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/24980613", "evidence_list": [ { "evidence": "RASSF1 was methylated in 45% of prostate cancer urine samples with methylation intensity significantly higher in prostate cancer than in benign prostatic hyperplasia cases (p = 0.018). In a univariate model RASSF1 methylation and the total number of methylated genes in prostate cancer tissue were predictive of time to biochemical recurrence (p = 0.019 and 0.043, respectively). On multivariate analysis RASSF1 methylation together with pathological stage was the most significant predictor of biochemical recurrence in patients with Gleason score 6 tumors when analyzed in tissue and urine (p ‚â§0.001)." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0001088" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, "synonyms": [ { "id": "DOID:10283", "name": "prostate neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "NGP - new growth of prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "tumor of the prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostate cancer, familial", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostatic neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "malignant tumor of the prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "hereditary prostate cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostatic cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" } ] }, "evidence_source": [ { "id": "24980613", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/24980613", "evidence_list": [ { "evidence": "RASSF1 was methylated in 45% of prostate cancer urine samples with methylation intensity significantly higher in prostate cancer than in benign prostatic hyperplasia cases (p = 0.018). In a univariate model RASSF1 methylation and the total number of methylated genes in prostate cancer tissue were predictive of time to biochemical recurrence (p = 0.019 and 0.043, respectively). On multivariate analysis RASSF1 methylation together with pathological stage was the most significant predictor of biochemical recurrence in patients with Gleason score 6 tumors when analyzed in tissue and urine (p ‚â§0.001)." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Prognostic value of RASSF1 promoter methylation in prostate cancer.", "journal": "The Journal of urology", "authors": "Daniunaite K, Jarmalaite S, Kalinauskaite N, Petroska D, Laurinavicius A, Lazutka JR, Jankevicius F", "date": "2014-07-02", "evidence": [], "reference": [ { "id": "24980613", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/24980613" } ] } ], "biomarker_canonical_id": "AN6722", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6723-1", "biomarker_component": [ { "biomarker": "increased PLAT aggregation", "assessed_biomarker_entity": { "recommended_name": "Platelet aggregation", "synonyms": [ { "synonym": "anucleate thrombocyte" }, { "synonym": "blood platelet" }, { "synonym": "enucleate thrombocyte" } ] }, "assessed_biomarker_entity_id": "CO:CL_0000233", "assessed_entity_type": "cell", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "11125-2" } ], "evidence_source": [ { "id": "7829253", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/7829253", "evidence_list": [ { "evidence": "Platelets significantly increased the invasiveness of the 3 types of mammalian tumor cell tested (MDA-MB231, MCF-7 and ZR-51). This increased invasiveness is due, at least partially, to an increase in gelatinase secretion. 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Overall, three high-mannose N-glycans (F0H6N2S0, F0H7N2S0, F0H8N2S0) exhibited significant diagnostic accuracy in both breast cancer cells and tissues, suggesting their potential role in biomarkers." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000479" } ] } ] } ], "best_biomarker_role": [ { "role": "diagnostic" } ], "condition": { "id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "name": "breast cancer", "description": "A thoracic cancer that originates in the mammary gland.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, "synonyms": [ { "id": "DOID:1612", "name": "malignant tumor of the breast", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "breast tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "mammary cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "primary breast cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "mammary tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "malignant neoplasm of breast", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" } ] }, "evidence_source": [ { "id": "30889355", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30889355", "evidence_list": [ { "evidence": "In comparing the N-glycan profiles of healthy individuals with those suffering from breast cancer, six N-glycans with AUC greater than 0.9 indicated excellent diagnostic accuracy (Figure 4). Of those, two bisected N-glycans (F0H4N5S0 and F1H4N5S0, Figure 4A,B) exhibited decreased relative abundances, while the other four N-glycans included three high-mannose N-glycans (F0H6N2S0, F0H7N2S0, and F0H8N2S0, Figure 4C,D,E), and fucosylated glycan (F1H3N2S0, Figure 4F) exhibited increased relative abundances. Overall, three high-mannose N-glycans (F0H6N2S0, F0H7N2S0, F0H8N2S0) exhibited significant diagnostic accuracy in both breast cancer cells and tissues, suggesting their potential role in biomarkers." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Comprehensive N-Glycome Profiling of Cells and Tissues for Breast Cancer Diagnosis.", "journal": "Journal of proteome research", "authors": "Li Q, Li G, Zhou Y, Zhang X, Sun M, Jiang H, Yu G", "date": "2019-03-20", "evidence": [], "reference": [ { "id": "30889355", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/30889355" } ] } ], "biomarker_canonical_id": "AN6741", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "c": "condition", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6742-1", "biomarker_component": [ { "biomarker": "increased N-glycan level", "assessed_biomarker_entity": { "recommended_name": "Neu5Gc", "synonyms": [] }, "assessed_biomarker_entity_id": "GTC:G26366JF", "assessed_entity_type": "glycan", "specimen": [ { "name": "blood", "id": "UBERON:0000178", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000178", "loinc_code": "" } ], "evidence_source": [ { "id": "35346112", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/35346112", "evidence_list": [ { "evidence": "Analysis of sera from breast cancer cases revealed significantly elevated levels of Neu5Gc biomarkers at all stages of breast cancer. We show that Neu5Gc serum biomarker levels can discriminate breast cancer patients from cancer-free individuals with 98.96% sensitivity and 100% specificity. Neu5Gc serum biomarkers are a promising new tool for early detection and disease monitoring for breast cancer that may complement current imaging- and biopsy-based approaches." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000178" } ] } ] } ], "best_biomarker_role": [ { "role": "monitoring" } ], "condition": { "id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "name": "breast cancer", "description": "A thoracic cancer that originates in the mammary gland.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, "synonyms": [ { "id": "DOID:1612", "name": "malignant tumor of the breast", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "breast tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "mammary cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "primary breast cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "mammary tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" }, { "id": "DOID:1612", "name": "malignant neoplasm of breast", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_1612" } ] }, "evidence_source": [ { "id": "35346112", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/35346112", "evidence_list": [ { "evidence": "Analysis of sera from breast cancer cases revealed significantly elevated levels of Neu5Gc biomarkers at all stages of breast cancer. We show that Neu5Gc serum biomarker levels can discriminate breast cancer patients from cancer-free individuals with 98.96% sensitivity and 100% specificity. Neu5Gc serum biomarkers are a promising new tool for early detection and disease monitoring for breast cancer that may complement current imaging- and biopsy-based approaches." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "N-glycolylneuraminic acid serum biomarker levels are elevated in breast cancer patients at all stages of disease.", "journal": "BMC cancer", "authors": "Shewell LK, Day CJ, Kutasovic JR, Abrahams JL, Wang J, Poole J, Niland C, Ferguson K, Saunus JM, Lakhani SR, von Itzstein M, Paton JC, Paton AW, Jennings MP", "date": "2022-03-30", "evidence": [], "reference": [ { "id": "35346112", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/35346112" } ] } ], "biomarker_canonical_id": "AN6742", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "w": "weight", "c": "condition", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6743-1", "biomarker_component": [ { "biomarker": "hypermethylated MIR-9-1 gene", "assessed_biomarker_entity": { "recommended_name": "miRNA 9-1 gene", "synonyms": [] }, "assessed_biomarker_entity_id": "MRB:MI0000466", "assessed_entity_type": "miRNA", "specimen": [ { "name": "ovary", "id": "UBERON:0000992", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0000992", "loinc_code": "" } ], "evidence_source": [ { "id": "29313235", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/29313235", "evidence_list": [ { "evidence": "...five microRNA genes (MIR-9-1, MIR-9-3, MIR-107, MIR-1258, and MIR-130b) methylated in the majority of tumor specimens in comparison with paired specimens of histologically intact tissue (37-57% vs. 4-9%, p<0.01). Methylation of three genes (MIR-9-1, MIR-9-3, and MIR-130b) was significantly (p‚â§0.05) associated with the parameters of ovarian cancer progress (clinical stage, differentiation degree, tumor size, and presence of metastases). These findings attest to oncosuppressive role of the studied microRNA genes (MIR-9-1, MIR-9-3, MIR-107, MIR-1258, and MIR-130b) in the pathogenesis and progress of ovarian cancer and indicated their prognostic potential." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0000992" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:2394", "recommended_name": { "id": "DOID:2394", "name": "ovarian cancer", "description": "A female reproductive organ cancer that is located_in the ovary.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, "synonyms": [ { "id": "DOID:2394", "name": "primary ovarian cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "tumor of the Ovary", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "ovary neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "malignant tumour of ovary", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "malignant Ovarian tumor", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" }, { "id": "DOID:2394", "name": "ovarian neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_2394" } ] }, "evidence_source": [ { "id": "29313235", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/29313235", "evidence_list": [ { "evidence": "...five microRNA genes (MIR-9-1, MIR-9-3, MIR-107, MIR-1258, and MIR-130b) methylated in the majority of tumor specimens in comparison with paired specimens of histologically intact tissue (37-57% vs. 4-9%, p<0.01). Methylation of three genes (MIR-9-1, MIR-9-3, and MIR-130b) was significantly (p‚â§0.05) associated with the parameters of ovarian cancer progress (clinical stage, differentiation degree, tumor size, and presence of metastases). These findings attest to oncosuppressive role of the studied microRNA genes (MIR-9-1, MIR-9-3, MIR-107, MIR-1258, and MIR-130b) in the pathogenesis and progress of ovarian cancer and indicated their prognostic potential." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Five Hypermethylated MicroRNA Genes as Potential Markers of Ovarian Cancer.", "journal": "Bulletin of experimental biology and medicine", "authors": "Braga EA, Loginov VI, Burdennyi AM, Filippova EA, Pronina IV, Kurevlev SV, Kazubskaya TP, Kushlinskii DN, Utkin DO, Ermilova VD, Kushlinskii NE", "date": "2018-01-10", "evidence": [], "reference": [ { "id": "29313235", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/29313235" } ] } ], "biomarker_canonical_id": "AN6743", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 }, { "biomarker_id": "AN6744-1", "biomarker_component": [ { "biomarker": "hypermethylated RASSF1 gene", "assessed_biomarker_entity": { "recommended_name": "Ras association domain-containing protein 1 gene", "synonyms": [ { "synonym": "123F2" }, { "synonym": "NORE2A" }, { "synonym": "RASSF1A" }, { "synonym": "RDA32" }, { "synonym": "REH3P21" } ] }, "assessed_biomarker_entity_id": "NCBI: 11186", "assessed_entity_type": "gene", "specimen": [ { "name": "urine", "id": "UBERON:0001088", "name_space": "Uberon", "url": "http://purl.obolibrary.org/obo/UBERON_0001088", "loinc_code": "" } ], "evidence_source": [ { "id": "24980613", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/24980613", "evidence_list": [ { "evidence": "Hypermethylation of RASSF1 in cancerous tissue and urine from patients with prostate cancer correlated with biochemical recurrence after radical prostatectomy. The prognostic potential of this biomarker deserves further investigation." } ], "tags": [ { "tag": "biomarker" }, { "tag": "assessed_biomarker_entity" }, { "tag": "specimen:UBERON:0001088" } ] } ] } ], "best_biomarker_role": [ { "role": "prognostic" } ], "condition": { "id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate.", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, "synonyms": [ { "id": "DOID:10283", "name": "prostate neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "NGP - new growth of prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "tumor of the prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostate cancer, familial", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostatic neoplasm", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "malignant tumor of the prostate", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "hereditary prostate cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" }, { "id": "DOID:10283", "name": "prostatic cancer", "resource": "Disease Ontology", "url": "http://purl.obolibrary.org/obo/DOID_10283" } ] }, "evidence_source": [ { "id": "24980613", "database": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/24980613", "evidence_list": [ { "evidence": "Hypermethylation of RASSF1 in cancerous tissue and urine from patients with prostate cancer correlated with biochemical recurrence after radical prostatectomy. The prognostic potential of this biomarker deserves further investigation." } ], "tags": [ { "tag": "best_biomarker_role" }, { "tag": "condition" } ] } ], "citation": [ { "title": "Prognostic value of RASSF1 promoter methylation in prostate cancer.", "journal": "The Journal of urology", "authors": "Daniunaite K, Jarmalaite S, Kalinauskaite N, Petroska D, Laurinavicius A, Lazutka JR, Jankevicius F", "date": "2014-07-02", "evidence": [], "reference": [ { "id": "24980613", "type": "Pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/24980613" } ] } ], "biomarker_canonical_id": "AN6744", "score": 1, "score_info": { "contributions": [ { "c": "first_pmid", "w": 1, "f": 1 }, { "c": "other_pmid", "w": 0.2, "f": 0 }, { "c": "first_source", "w": 1, "f": 0 }, { "c": "other_source", "w": 0.1, "f": 0 }, { "c": "generic_condition_pen", "w": -4, "f": 0 }, { "c": "loinc", "w": 1, "f": 0 } ], "formula": "sum(w*f)", "variables": { "c": "condition", "w": "weight", "f": "frequency" } }, "collision": 0 } ]