{ "assessed_biomarker_entity": "UroMark bladder cancer 150 CpG loci methylation assay panel", "assessed_entity_type": "gene", "components": { "protein": [ { "accession": "Q6P1J9-1", "name": "Parafibromin", "evidence": [ { "id": "GLY_000625", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000625" }, { "id": "28163793", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28163793" } ] } ], "glycan": [] }, "instances": [ { "best_biomarker_type": "diagnostic", "status": "increased 150 CpG loci methylation", "notes": "FDA approval for detection of bladder cancer but not approved for stand-alone test to replace cystoscopy|list of specific UroMark CpG methylation loci is available at PMID:28163793, Additional file 1: Table S4, dx.doi.org/10.1186/s13148-016-0303-5 (12/02/2022)", "literature_evidence": "We defined a 150 CpG loci biomarker panel from a cohort of 86 muscle-invasive bladder cancers and 30 normal urothelium. Based on this panel, we developed the UroMark assay, a next-generation bisulphite sequencing assay and analysis pipeline for the detection of bladder cancer from urinary sediment DNA. The UroMark panel was defined using pre-set criteria in the training cohort (Table 1) as follows: in order for probes to be considered as potential biomarker candidates, they had to show no or very low methylation (beta <10%) in normal urothelium, blood and non-cancer urine samples and methylation (beta) of >50% in bladder cancer. A <10% cut was selected from the analysis of beta values from fully unmethylated control DNA. The probes passing this filter were subsequently used to generate a classifier using a random forest model. [PMID:28163793]", "loinc_code": "", "tissue": { "name": "urine", "namespace": "UBERON", "id": "0001088", "url": "http://purl.obolibrary.org/obo/UBERON_0001088" }, "disease": { "disease_id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder." }, "synonyms": [ { "id": "DOID:11054", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:11054", "name": "bladder cancer", "description": "" }, { "id": "DOID:11054", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:11054", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "A primary or metastatic malignant neoplasm involving the bladder." }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "bladder cancer, somatic", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "cancer of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumor", "description": "" }, { "id": "MIM:109800", "resource": "MIM", "url": "https://www.omim.org/entry/109800", "name": "Bladder cancer", "description": "Bladder cancer" } ] }, "evidence": [ { "id": "GLY_000625", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000625" }, { "id": "28163793", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28163793" } ] } ], "publication": [ { "title": "UroMark-a urinary biomarker assay for the detection of bladder cancer.", "journal": "Clinical epigenetics", "authors": "Feber Andrew, Dhami Pawan, Dong Liqin, de Winter Patricia, Tan Wei Shen, Mart\u00ednez-Fern\u00e1ndez M\u00f3nica, Paul Dirk S, Hynes-Allen Antony, Rezaee Sheida, Gurung Pratik, Rodney Simon, Mehmood Ahmed, Villacampa Felipe, de la Rosa Federico, Jameson Charles, Cheng Kar Keung, Zeegers Maurice P, Bryan Richard T, James Nicholas D, Paramio Jesus M, Freeman Alex, Beck Stephan, Kelly John D", "date": "2017", "reference": [ { "type": "PubMed", "id": "28163793", "url": "https://glygen.org/publication/PubMed/28163793" } ], "evidence": [ { "id": "GLY_000625", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000625" } ] } ], "evidence": [ { "id": "GLY_000625", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000625" }, { "id": "28163793", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28163793" } ], "biomarker_id": "A0479", "aclist": [ "Q6P1J9-1" ], "crossref": [], "section_stats": [ { "table_id": "instances", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "best_biomarker_type", "status", "notes", "literature_evidence", "loinc_code", "tissue.name", "tissue.namespace", "tissue.id", "tissue.url", "disease.disease_id" ] }, { "table_id": "components", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "authors", "date" ] } ] }