
==== Front
JCO Precis Oncol
JCO Precis Oncol
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PO
JCO Precision Oncology
2473-4284
Wolters Kluwer Health

39259913
PO.24.00301
10.1200/PO.24.00301
00206
ORIGINAL REPORTS
Cancer Genetics
Clinical Utility of Molecular Tumor Board Review for Identification of Possible Germline Pathogenic Variants on Tumor Next-Generation Sequencing Reports
https://orcid.org/0000-0003-1084-6678
Rives Taylor A. MD 1
https://orcid.org/0000-0003-4930-7188
Collard James BS 2
https://orcid.org/0000-0002-9383-7381
Li Ning MS 3
https://orcid.org/0000-0002-5111-9437
Yan Donglin PhD 3
Dietrich Charles S. MD 1 2
https://orcid.org/0000-0002-9417-6642
Miller Rachel W. MD 1 2
https://orcid.org/0000-0003-1213-7509
Ueland Frederick R. MD 1 2
Pickarski Justine MS, LGC 2
https://orcid.org/0000-0001-8575-4546
Kolesar Jill M. PharmD 1 2 4
1 Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Kentucky, Lexington, KY
2 Markey Cancer Center, University of Kentucky, Lexington, KY
3 Department of Biostatistics, College of Public Health, University of Kentucky, Lexington, KY
4 College of Pharmacy, University of Kentucky, Lexington, KY
Jill M. Kolesar, PharmD; e-mail: jill-kolesar@uiowa.edu.
2024
11 9 2024
11 9 2024
8 e24003017 5 2024
10 7 2024
31 7 2024
© 2024 by American Society of Clinical Oncology
2024
American Society of Clinical Oncology
https://creativecommons.org/licenses/by-nc-nd/4.0/ Creative Commons Attribution Non-Commercial No Derivatives 4.0 License: http://creativecommons.org/licenses/by-nc-nd/4.0/

PURPOSE

Tumor next-generation sequencing (NGS) testing identifies possible germline pathogenic variants (PGPVs), creating a dilemma for appropriate recognition, triage, and management. The objective of this study was to determine the clinical utility of an institutional molecular tumor board (MTB) in assessing tumor NGS reports for PGPVs.

METHODS

Our institutional MTB reviews all NGS reports to provide treatment and further testing recommendations, including genetic counseling referral and consideration of genetic testing (GC/GT). We studied the patients reviewed by the MTB who were recommended for GC/GT to determine the frequency of referral to a GC, germline test completion, rate of pathogenic germline variants (PGVs), factors related to PGVs, and germline conversion rate (GCR).

RESULTS

Of the 2,355 patients reviewed by the MTB during the study period, 609 (25.9%) had a recommendation for GC/GT. Of the 609 with a GC/GT recommendation, only 181 (29.7%) were referred for GC/GT by their treating physicians, and only 107 (17.6%) completed GT. Of the 107 patients completing GT, 29 (26%) had a confirmed PGV. The only factors significantly associated with PGVs were testing due to a PGPV and higher mean variant allele fraction on the tumor NGS. Only 40 patients with a GC/GT recommendation (14.3%) due to a PGPV completed GT; however, the GCR was 42.5% (n = 17/40).

CONCLUSION

The MTB review of PGPV is clinically valuable, identifying PGPV in 12% of patients undergoing tumor NGS and a GCR of 42.5%. Rates of GC/GT completion were relatively low due to under-referral by treating physicians. Given the high GCR, the authors encourage institutional algorithms to help increase GC/GT rates for patients found to have PGPV following tumor NGS testing.

OPEN-ACCESSTRUE
==== Body
pmcINTRODUCTION

Hereditary predisposition accounts for 4%-24% of all cancers, although the rate varies by cancer type.1 Identification of pathogenic germline variants (PGVs) in patients and their family members can affect cancer outcomes, screening opportunities, and risk reduction strategies and expand cancer treatment options.2 The current approach to identify patients with inherited cancer risk is based on clinical factors such as cancer type, age at diagnosis, and family history. Universal germline testing (GT) is standard for many cancers, including ovarian, pancreatic, paragangliomas, and pheochromocytomas.3-5 Emerging evidence suggests that more cancers are associated with PGVs that have not historically been associated with hereditary cancer syndromes, indicating the need to identify patients with hereditary risk beyond the current clinical factors.1,6,7 Furthermore, in one large analysis of patients with advanced cancer, 8% of patients had a therapeutically actionable PGV, and of those, 40% received PGV-directed therapy.8

CONTEXT

Key Objective

Can an institutional molecular tumor board (MTB) review of next-generation sequencing (NGS) improve recognition and management of possible germline pathogenic variants (PGPVs)?

Knowledge Generated

In this single-institution study, MTB review of NGS tumor testing identified PGPVs in 12% of patients with a high germline conversion rate in those who underwent genetic counseling referral and consideration of genetic testing (GC/GT). GC/GT rates remain low due to provider under-referral despite MTB recommendation for GC/GT.

Relevance

An institutional MTB review of all NGS reports is an option to identify and manage PGPVs. Ultimately, this uses a genetic counselor to review all NGS reports for PGPV and can increase the rate of guideline-compliant PGPV recognition while offloading busy clinicians who are not accustomed to recognizing PGPVs on NGS reports.

In addition to standard GT, the rise of tumor next-generation sequencing (NGS) has introduced another avenue for the detection of hereditary risk via possible germline pathogenic variants (PGPVs) identified within tumor NGS. Guidelines recommend that patients receive counseling about the possibility of identifying PGPVs with tumor NGS.3,4,9 The American College of Medical Genomics and Genetics (ACMG) recommends that clinical laboratories report secondary findings in medically actionable genes incidentally discovered during clinical whole-genome and whole-exome sequencing, and many of these genes are included as part of tumor NGS testing.10 Furthermore, the European Society of Medical Oncology (ESMO) Precision Medicine Working Group recommends GC/GT for PGPVs identified in 40 genes on the basis of a germline conversion rate (GCR) of >5%.11 National Comprehensive Cancer Network (NCCN) guidelines state that GC/GT is indicated if a pathogenic/likely pathogenic variant identified on tumor genomic testing has implications if also identified in the germline; therefore, all patients who have a PGPV also meet NCCN criteria for GC/GT.3 Despite these recommendations, patients are rarely counseled before tumor NGS, and PGPVs are not reported in the NGS reports by most testing laboratories. This requires treating physicians to both recognize and manage PGPVs without support or training. To assist with the identification and management of patients with a hereditary risk of cancer, our institutional molecular tumor board (MTB) includes a genetic counselor with primary responsibility for identifying PGPVs and recommending GC/GT.

The primary goal of this study was to assess the clinical utility of an institutional MTB for the recognition and management of PGPVs.

METHODS

Study Design and Setting

This is a retrospective evaluation of patients reviewed by the University of Kentucky Markey Cancer Center MTB. The MTB reviews all patients undergoing tumor NGS at Markey Cancer Center and consists of surgical oncologists, medical oncologists, pathologists, pharmacists, and a genetic counselor. The MTB makes recommendations to treating physicians for treatment on the basis of mutation profile, as well as recommendations for additional testing; however, treating physicians are responsible for treatment and testing decisions. A letter is emailed to the treating physician with recommendations and uploaded into the electronic health record. At the time of review, patient demographics, mutations, and MTB recommendations are recorded in an internal database (LabKey, Seattle, WA).

Patient Selection and Collection Process

All patients reviewed by the MTB between January 14, 2019, and December 21, 2022, who received a recommendation for GT are included in this analysis. The treating physician ordered the tumor NGS per clinical preference; therefore, several external testing companies were used in this analysis. The most frequently used NGS assays at our institution during the time of this study were FoundationOne TissueCDx, Caris MiProfile, and Guardant 360. Due to the retrospective nature, patients were not randomly assigned. Additional inclusion criteria required patients to be receiving oncology care at the University of Kentucky and be 18 years or older at the time of MTB review. Participants were unselected for family history, disease site, stage, age, or sex. This study followed the guidelines of the Declaration of Helsinki under the US Common Rule and was approved by our institutional review board (IRB, protocol code 88317) and received a waiver of consent.

GT Recommendations

Tumor NGS reports and clinical characteristics were reviewed for each patient by a genetic counselor, who made recommendations for GT during the MTB review. Reasons for GT included NCCN guideline-recommended clinical characteristics (tumor type, age of diagnosis, history of multiple cancers, family history) or presence of a somatic pathogenic variant or microsatellite instability in the NGS report concerning for PGPV. Genes that were considered concerning for PGPV included those with specific management recommendations from the NCCN or genes included on the ACMG Secondary Findings list, which are associated with hereditary cancers.10 Additionally, the MITF p.E318K pathogenic variant was included since it is a well-described germline variant.

Recommendations for GT were accompanied by evidence levels. Evidence level 1 defined GT as guideline-recommended and standard of care.3,4,9-12 For example, a patient with a BRCA2 variant detected on any tumor type warrants this level of evidence. Evidence level 2 defined GT as clinically and analytically valid, expert consensus-recommended testing. For example, a patient with a CDKN2A variant detected on a lung specimen in a patient with a family history of early-onset melanoma warrants this level of evidence. Evidence level 3 defined GT as clinically and analytically valid; consider testing if the clinical situation warrants. For example, a patient with a single FANCC variant detected on their specimen is given this level of evidence since this is associated with an autosomal recessive condition. Of note, evidence levels change over time as data continue to evolve. For example, we now give an evidence level 1 to all patients with triple-negative breast cancer on the basis of NCCN guidelines; however, during this study period, only patients age ≤60 years with this tumor type were given this level of evidence.

Data Collection

Demographic, clinicopathologic, germline, and somatic testing results were obtained for each patient. Most of the data were collected during active management of the patient during MTB review; however, the electronic medical record was also queried retrospectively to obtain additional information not available in the clinical database.

Similar cancer types with smaller sample sizes were grouped. Other GI cancers (Other GI) were defined as noncolorectal, esophageal, or pancreatic cancer types and included stomach, small intestine, appendiceal, and hepatobiliary cancers. The ovarian group also included fallopian tube and primary peritoneal cancers. Uterine/gynecologic (GYN) included uterine, cervix, vulvar, and vaginal cancers. Genitourinary (GU) cancers were defined as nonprostate GU cancers and included bladder, kidney, ureteral, and testis. The Other category included cancers with small numbers, including eye, adrenal, unknown primary, oral, or pharyngeal cancer. Patients were assigned to categories by sex assigned at birth. All patients except one were cisgender.

Study Objectives

The primary objective was to determine the clinical utility of MTB, defined as the rate of PGPVs identified by the MTB and the GCR between tumor NGS PGPVs and germline results. Additional outcomes include (1) frequency and rationale of germline recommendations, (2) frequency of GT after MTB recommendation, (3) factors associated with completing GT, and (4) factors associated with PGV.

Statistics

Descriptive statistics were used to summarize demographic and clinicopathologic characteristics and tumor NGS and GT results using chi-square and Fisher exact tests. Univariable and multivariable logistic regression analyses were used to identify factors that predict the completion of GT and factors associated with positive testing results. Exact logistic regression was used if there was a small observation number (0 < n < 5). Haldane-Anscombe correction was used by adding 0.5 to each cell if the observation number was 0. No sample size calculation was performed as this is a cohort study of patients reviewed by the MTB.

IRB Statement

The study was conducted in accordance with the Declaration of Helsinki and approved by the IRB of the University of Kentucky (protocol code 88317).

Informed Consent Statement

The requirement for patient consent was waived by the UK IRB.

RESULTS

There were 2,355 patients reviewed at MTB during the study period. In total, 609 (25.9%) patients received a recommendation for GC/GT and were included in this study (Fig 1). The mean age at the time of MTB review was 61.2 years (range, 18-87), most patients were White (n = 565, 92.8%), and 55% were assigned female at birth (n = 335), whereas 45% were assigned male at birth (n = 274; Data Supplement, Table S1). At the time of MTB review, most patients had either recurrent or persistent disease (n = 283, 46.5%), followed by newly diagnosed stage IV (n = 221, 36.3%), stage III (n = 60, 9.9%), stage II (n = 25, 4.1%), and stage I (n = 19, 3.1%) disease. The most frequent cancer types reviewed at MTB with a recommendation for GC/GT were colorectal (n = 106, 17.4%), ovarian (n = 72, 11.8%), lung (n = 70, 11.5%), breast (n = 54, 8.9%), and uterus/GYN (n = 42, 6.9%).

FIG 1. Flowsheet representing rate of germline testing recommendations, genetic counseling, and completion of germline testing. MTB, molecular tumor board; VUS, variant of unknown significance.

Of the 609 patients with a recommendation for GC/GT, only 17.6% (n = 107) completed GT (Fig 1). Of these, 199 patients were recommended due to PGPV alone (32.7%), 80 patients were recommended due to PGPV and clinical factors (13.1%), and 330 patients were recommended due to clinical factors alone (54.2%). During the study period, 29.8% of patients (n = 181) were referred to GC, and of those, 43.1% (n = 78) were referred after MTB recommendation. The other 103 patients (56.9%) were referred to GC by their treating physician before being reviewed by the MTB. Patient, MTB recommendation, and health care delivery factors were assessed as predictors of completing GT (Table 1). Patient factors predicting the completion of GT were assigned female sex at birth (P = .01) and tumor type (P = .02). The top five tumor types with the highest rate of completing GT were ovarian (26/72, 36.1%), breast (13/54, 24.1%), uterine/GYN (10/24, 23.8%), colorectal (20/106, 18.9%), and esophageal (3/17, 17.7; Data Supplement, Table S2). The only significant MTB recommendation factor was evidence level, with stronger level of evidence associated with increased testing (P = .0005). In contrast, every health care delivery factor evaluated was strongly and significantly associated with completing testing, including treating physician (P ≤ .0001), receiving a GC/GT referral (P = .0001), MTB recommendation for GC/GT referral (P = .0009), and being seen by the GC (.0001). The rate of GT varied significantly between the treating physicians with a range of 0%-57.6% (P < .0001; Data Supplement, Table S2).

TABLE 1. Patient, Recommendation, and Process of Care Factors Associated With Completed Testing

Factors Associated With Testing	Patients Without Testing (n = 502)	Patients With Testing (n = 107)	P a	
Patient factors				
 Age at MTB review, mean (range)	61.42 (18-87)	59.9 (28-86)	.29	
 Sex assigned at birth, No. (%)			.01	
  Female	264 (52.59)	71 (66.36)	
  Male	238 (47.41)	36 (33.64)	
 Race, No. (%)			.58	
  White	466 (92.83)	99 (92.52)	
  Black	25 (4.98)	4 (3.74)	
  Asian	4 (0.8)	2 (1.87)	
  Native Hawaiian/Pacific Islander	3 (0.6)	0	
  Hispanic	3 (0.6)	2 (1.87)	
  Unknown	1 (0.1)	0	
 Diagnosis site, No. (%)			.02	
  Colorectal	86 (17.13)	20 (18.69)	
  Ovarian	46 (9.16)	26 (24.3)	
  Lung	64 (12.75)	6 (5.61)	
  Breast	41 (8.17)	13 (12.15)	
  Uterus/GYN	32 (6.37)	10 (9.35)	
  Other GI	35 (6.97)	6 (5.61)	
  Pancreas	33 (6.57)	7 (6.54)	
  Prostate	31 (6.18)	6 (5.61)	
  GU/bladder	30 (5.98)	1 (0.93)	
  Skin	21 (4.18)	3 (2.8)	
  Thyroid	20 (3.98)	3 (2.8)	
  Esophagus	14 (2.79)	3 (2.8)	
  Brain/spinal cord	16 (3.19)	1 (0.93)	
  Bone/soft tissue	14 (2.79)	0	
  Other	19 (3.78)	2 (1.87)	
 Stage, No. (%)			.1	
  Unknown	1 (0.2)	0	
  Stage I	16 (3.19)	3 (2.8)	
  Stage II	20 (3.98)	5 (4.67)	
  Stage III	43 (8.57)	17 (15.89)	
  Stage IV	177 (35.26)	44 (41.12)	
  Recurrent/persistent	245 (48.8)	38 (35.51)	
MTB recommendation factors, No. (%)				
 Review type			.15	
  Asynchronous	412 (82.07)	94 (87.85)	
  In person meeting	90 (17.93)	13 (12.15)	
 Evidence level			.0005	
  1	403 (80.28)	104 (97.2)	
  2	85 (16.93)	3 (2.8)	
  3	14 (2.79)	0	
 Reason for GC/GT by MTB			.055	
  PGPVb	239 (47.61)	40 (37.38)	
  Other indication	263 (52.39)	67 (62.62)	
Healthcare delivery factors, No. (%)				
 Physicians			<.0001	
  Physician 1	91 (18.13)	21 (19.63)	
  Physician 2	49 (9.76)	8 (7.48)		
  Physician 3	39 (7.77)	8 (7.48)	
  Physician 4	28 (5.58)	15 (14.02)	
  Physician 5	14 (2.79)	19 (17.76)	
  Physician 6	28 (5.58)	1 (0.93)	
  Physician 7	23 (4.58)	3 (2.8)	
  Physician 8	21 (4.18)	4 (3.74)	
  Physician 9	21 (4.18)	3 (2.8)	
  Physician 10	22 (4.38)	2 (1.87)	
  Physician 11	15 (2.99)	6 (5.61)	
  Physician 12	18 (3.59)	2 (1.87)	
  Physician 13	14 (2.79)	4 (3.74)	
  Physician 14	14 (2.79)	2 (1.87)	
  Physician 15	15 (2.99)	0	
  Physician 16	11 (2.19)	0	
  Other	78 (15.54)	9 (8.41)	
 Referred			.0001	
  No	427 (85.23)	0	
  Yes	74 (14.77)	107 (100)	
 Referred after MTB recommendation			.0009	
  No	53 (70.27)	50 (46.73)	
  Yes	21 (29.73)	57 (53.28)	
 Seen by GC			.0001	
  No	487 (97.21)	0	
  Yes	14 (2.79)	107 (100)	
Abbreviations: GC, genetic counseling; GT, genetic testing; GU, genitourinary; GYN, gynecologic; MTB, molecular tumor board; PGPV, possible germline pathogenic variant.

a Haldane-Anscombe correction was used for data cells with zero observations by adding 0.5 to each cell.

b Patients were assigned to PGPV if they had an indication for testing due to a PGPV, regardless of whether they had additional indications.

Of the 107 patients with GT results, 27.1% (n = 29) had a PGV identified, 57% (n = 61) had negative GT, and 15.9% (n = 17) had a variant of unknown significance (VUS; Table 2). Of the 107 patients with germline results, 21 patients were recommended due to PGPV alone (19.6%), 19 patients were recommended due to PGPV and clinical factors (17.8%), and 67 patients were recommended due to clinical factors alone (62.6%). Five patients had at least one relative undergo cascade testing through our facility after the patient's PGV was identified. Patient, MTB recommendation, and health care delivery factors were also assessed as predictors of test positivity; the only two factors associated with positive GT were the presence of PGPV (P < .001) and higher mean variant allele fraction (VAF; P = .027; Table 2). Of the 29 patients who had positive GT, 34.5% (n = 10) had a GC/GT recommendation due to the identification of a PGPV on somatic testing, 11 patients were recommended due to PGPV and clinical factors (37.9%), and eight patients were recommended due to clinical factors alone (27.6%).

TABLE 2. Germline Testing Results and Patient, Recommendation, and Process of Care Factors Associated With Positive Testing

Testing Results and Factors Associated With Positive Testing	Patients With Positive Testing (n = 29)	Patients With Negative/VUS Testing (n = 78)	P	
Outcome of germline testing results, No. (%)				
 Germline result			NA	
  Positive	29 (100)	0	
  Negative	0	61 (78.2)	
  VUS	0	17 (21.8)	
 Number of positive germline pathogenic variants			NA	
  0	0	78 (100)	
  1	26 (89.7)	0	
  2	3 (10.3)	0	
 Cascade testing			NA	
  Yes	5 (17.2)	0	
  No	24 (82.8)	78 (100)	
Patient factors				
 Age at MTB review, mean (range)	56.79 (31-86)	61.05 (28-85)	.17	
 Sex assigned at birth, No. (%)			.14	
  Female	16 (55.17)	55 (70.51)	
  Male	13 (44.83)	23 (29.49)	
 Race, No. (%)			.76a	
  White	29 (100)	70 (89.74)	
  Black	0	4 (5.13)	
  Asian	0	2 (2.56)	
  Hispanic	0	2 (2.56)	
 Diagnosis site, No. (%)			.66a	
  Ovarian	6 (20.69)	20 (25.64)	
  Colorectal	3 (10.34)	17(21.79)	
  Uterus/GYN	3 (10.34)	7 (8.97)	
  Prostate	3 (10.34)	3 (3.85)	
  Lung	3 (10.34)	3 (3.85)	
  Thyroid	3 (10.34)	0	
  Breast	2 (6.9)	11 (14.1)	
  Other GI	2 (6.9)	4 (5.13)	
  Pancreas	1 (3.45)	6 (7.69)	
  Esophagus	1 (3.45)	2 (2.56)	
  Skin	1 (3.45)	2 (2.56)	
  Brain/spinal cord	1 (3.45)	0	
  GU/bladder	0	1 (1.28)	
  Adrenal	0	1 (1.28)	
  Eye	0	1 (1.28)	
 MTB stage, No. (%)			.77a	
  Stage I	1 (3.45)	2 (2.56)	
  Stage II	2 (6.9)	3 (3.85)	
  Stage III	6 (20.69)	11 (14.1)	
  Stage IV	10 (34.48)	34 (43.59)	
  Recurrent/persistent	10 (34.48)	28 (35.9)	
MTB recommendation factors				
 Review type, No. (%)			.73	
  Asynchronous	26 (89.66)	68 (87.18)	
  In person meeting	3 (10.34)	10 (12.82)	
 Evidence level, No. (%)			.16	
  1	27(93.1)	77 (98.72)	
  2	2 (6.9)	1 (1.28)	
 Reason for germline testing recommendation by MTB, No. (%)			<.0001	
  PGPVb	21 (72.41)	19 (24.36)	
  Other	8 (27.59)	59 (75.64)	
 Mean VAF, % (range)	41.4 (5-93)	54.8 (41-78)	.027	
Healthcare delivery factors, No. (%)				
 Physicians			.55a	
  Physician 1	6 (20.69)	15 (19.23)	
  Physician 5	4 (13.79)	15 (19.23)	
  Physician 4	2 (6.9)	13 (16.67)	
  Other physicians	17 (58.62)	35 (44.87)	
Abbreviations: GU, genitourinary; GYN, gynecologic; MTB, molecular tumor board; NA, not available; PGPV, possible germline pathogenic variant; VAF, variant allele fraction; VUS, variant of unknown significance.

a Haldane-Anscombe correction was used for data cells with zero observations by adding 0.5 to each cell.

b Patients were assigned to PGPV if they had an indication for testing due to a PGPV, regardless of whether they had additional indications.

Among the 2,355 patients reviewed by the MTB over the study period, 279 (12%) had a PGPV identified on tumor NGS. The most common genetic alterations prompting a recommendation for GT were ATM (21.5%, n = 65), BRCA2 (10.6%, n = 32), high microsatellite instability (7.3%, n = 22), CHEK2 (6.6%, n = 20), and BRCA1 (5.9%, n = 18; Fig 2). There were 17 patients who had more than one PGPV detected: 12 patients had two PGPVs, three patients had three PGPVs, one patient had five PGPVs, and one patient had seven PGPVs.

FIG 2. Genes that prompted recommendation for germline testing. Other genes included the following: AXIN2, BAP1, BARD1, BMPR1A, CDH1, CDKN2A/B, CTNNA1, EGFR, FANCA, FANCC, FH, FLCN, HOXB13, LZTR1, MEN1, MITF, MLH1, MSH2, NBN, NF1, NF2, PALB2, POLE, PMS2, RAD50, RAD51C, RAD51D, RET, SDHB, SDHC, SMARCA4, TMEM127, TP53, TSC2, VHL.

Of the patients with GC/GT recommendation due to a PGPV, only 40 patients (14.3%) completed GT; however, the GCR/concordance was 42.5% (n = 17/40). The majority of patients with a GC/GT recommendation (60%) underwent MiProfile (Caris) testing (24/40), 35% (14/40) were tested with TissueCDx (FoundationOne), and 5% (2/40) underwent testing by Guardant360CDx. The NGS report only explicitly recommended GT for BRCA1/2 and VHL (MiProfile) and Lynch syndrome (Tissue CDx). Deeper in the NGS reports in the gene descriptions, some noted germline associations of genes with hereditary cancer syndromes but did not recommend GT (MSH6, CHEK2, PALB2, ATM, MUTYH, MITF, PTEN, MLH2, RAD51C, MEN1). The NGS reports did not note any germline associations for FLCN, BAP1, and CDNK2A. In January 2021, TissueCDx reports began notating whether there were any PGPVs detected on a tumor specimen. Before this, the labs used did not note whether PGPVs were detected; therefore, the PGPVs reported varied significantly and depended on testing date. The eight genes with concordant pathogenic variants between tumor and germline were ATM, BRCA2, CHEK2, MITF, MUTYH, PALB2, RAD51C, and VHL (Fig 3). There were only four mutation types associated with concordant germline pathogenic variants: frameshift, point mutation, splice site mutation, and truncations, and the mean VAF ranged from 41% to 78% (Table 3). Mutations not associated with concordant germline pathogenic variants included complete gene loss, deletions, and complex rearrangements. There were four additional patients (10%) with a PGV that differed from the PGPV identified on the tumor. Five patients with a PGV also had one VUS identified. Six patients with negative GT had at least one VUS identified, and two of those patients had two VUS identified. Thirteen patients had negative germline results.

FIG 3. Heat map of concordant germline and tumor pathogenic variants. GYN, gynecologic; MTB, molecular tumor board; PGPV, possible germline pathogenic variant.

TABLE 3. Summary of Genes With Concordant Pathogenic Variants Between Tumor and Germline

Gene/Mutation	Mutation Type	VAF, %	Tumor Type	
ATM				
 Splice site 8786 + 1G>A	Slice site	54	Other GI	
 E522fs*43	Truncation	41	Esophagus	
 Splice site 2921 + 1G>A	Splice site	78	Uterus/GYN	
 c.5320-5_5320-2delTCTA	Splice site	47	Skin	
 G1868*	Truncation	64	Prostate	
BRCA2				
 R2659K	Point mutation	45	Pancreas	
 V1804fs*2	Truncation	53	Lung	
 S884*	Truncation	57	Lung	
CHEK2				
 T367fs	Frameshift	46	Thyroid	
 T367fs	Frameshift	50	Colorectal	
 R177G	Point mutation	70	Lung	
PALB2				
 Q66*	Truncation	47	Ovarian	
 S254fs	Frameshift	57	Breast	
MITF				
 E318K	Point mutation	47	Colorectal	
MUTYH				
 G396D	Point mutation	43	Uterus/GYN	
RAD51C				
 Q33*	Truncation	76	Ovarian	
VHL				
 Y98S	Point mutation	58	Brain/spinal cord	
Abbreviations: GYN, gynecologic; VAF, variant allele fraction.

DISCUSSION

Tumor NGS is performed to identify targetable mutations and is now the standard of care for many cancers; however, it has created the dilemma of both recognizing and triaging possible germline findings, which are estimated to occur in 5%-16% of patients undergoing somatic tumor testing.7,13-16 One strategy for managing incidental findings is via an institutional MTB.17-20 In this study, the Markey Cancer Center MTB, with genetic counselor participation, assessed tumor NGS reports and identified 609 (12%) patients with a PGPV who received a recommendation for GC/GT. A similar study identified only 5% of patients in their population who would receive a recommendation for GC/GT; however, the genes prompting a recommendation in that study were more limited, which likely accounts for this difference.21 NGS reports only recommended GT for the most prominent hereditary cancer syndromes (BRCA1/2, Lynch syndrome, VHL) and only recently started reporting these; therefore, they are not reliable for identifying all PGPVs. This highlights the importance of implementing a strategy to recognize and act on these findings.

Despite frequent identification of PGPVs, rates of GC/GT completion were low. Only 30% of patients with a recommendation for GT were referred to GC/GT by their treating physician with a completion range of 0% (bone)-36% (ovarian). This is similar to national estimates of only 25% of eligible patients being referred, most commonly due to the lack of recognition of the need for GC/GT.22,23 In our study, providers were sent the MTB recommendation letter highlighting the need for GC/GT for their patients; however, only a minority of patients were referred. In a similar study, automatic GC/GT referral was developed for findings on tumor NGS; however, only 41% of all GC/GT referred patients completed testing.21 Significant predictors of completing GC/GT in our study were female sex assigned at birth, cancer type, strongest evidence supporting testing, treating physician, referral to GC, if referred on the basis of MTB recommendation, and patient attending the GC appointment. GC/GT completion was highest among cancers with routine recommendations for GC/GT, including GYN cancers (ovarian, uterine/GYN), breast cancer, and colorectal cancer, although completion rates were low for pancreas cancer at approximately 17.5%.

Notably, almost half of patients were referred to GC/GT after the MTB recommendation was made, which highlights the important role of MTB in reviewing NGS reports for PGPVs. Furthermore, MTB recommendation may be more important in cancer types where hereditary syndromes are historically less uncommon; for example, of the eight patients with lung cancer who were referred to GC, six (75%) of them were referred after MTB recommendation. Over 50% of patients (330/609) were recommended to have GC/GT due to clinical factors independent of their tumor NGS report (ie, cancer type, age at diagnosis, or family history) and had not been referred at the time of MTB review. These patients were previously missed by their treating physician as needing to be referred for GC/GT, and the MTB can assist in capturing these potential misses. In addition, 199 patients received a recommendation on the basis of the presence of PGPV alone, who would not have otherwise been a candidate for GT on the basis of clinical factors.

Of the patients who completed GT, 29 (27.1%) patients had a PGV identified. The only factors significantly associated with the identification of a PGV were a PGPV as the indication for testing and a higher mean VAF. Notably, clinical factors, including age, stage, gender, and disease type, were not associated with test positivity. The GCR between PGPV and a germline pathogenic variant was 42.5%. GCR varies by gene, and the ESMO Precision Medicine Working Group recently expanded their recommendations for follow-up of PGPVs to include 40 genes with a GCR of >5% as well as consideration of age of cancer diagnosis for certain genes.11,12 In this study, all concordant PGPV were included in the 40 genes recommended by ESMO except for MITF, although GCR for MITF was 100% (1/1), suggesting MTB review may augment ESMO recommendations for individual patients.24 Most of the genes included on the ESMO panel have US Food and Drug Administration–approved therapeutic relevance or consideration for off-label use. Furthermore, two patients (2/17, 11.8%) with concordant PGPVs were eligible for therapies that they would not have been a candidate for without positive GT (olaparib for germline BRCA mutations and belzutifan for germline VHL mutations).25,26

Despite notifying patients about the recommendations, the low rates of GC/GT referral in our study demonstrate the need for interventions to improve rates of GC/GT among appropriate patients. Lack of physician referral is the most common reason for not completing GC/GT; therefore, it warrants further study. Many individuals undergoing tumor NGS are patients with advanced-stage cancer requiring multiple oncology visits and complex care, which can be challenging to both patients and physicians when recommending additional appointments and follow-up tests, such as GT. Novel methods to deliver genomics care within health care systems are needed to improve rates of recommended GT effectively.

Strengths of this study include consecutive enrollment of participants, a relatively large sample size, primarily prospective collection of data, and the inclusion of a pan-cancer cohort. Study limitations are that it is a single-institution study, and most patients were non-Hispanic White. This limits the generalizability of the results although variant rates of GC/GT referral and GCR were similar to previous reports.

In conclusion, MTB review of PGPV has clinical utility, identifying PGPV in 12% of patients undergoing MTB and with a GCR of 42.5%. However, rates of GC/GT completion were low primarily due to under-referral by treating physicians. Given the high GCR, the authors encourage institutional algorithms to help increase GC/GT rates for patients found to have PGPV following tumor NGS testing.

SUPPORT

DATA SHARING STATEMENT

Anonymized data sets may be available upon request. Requests for access to data may be obtained by contacting the corresponding author.

AUTHOR CONTRIBUTIONS

Conception and design: Rachel W. Miller, Justine Pickarski, Jill M. Kolesar

Financial support: Jill M. Kolesar

Administrative support: Charles S. Dietrich, Justine Pickarski, Jill M. Kolesar

Provision of study materials or patients: Jill M. Kolesar

Collection and assembly of data: Taylor A. Rives, James Collard, Rachel W. Miller, Justine Pickarski, Jill M. Kolesar

Data analysis and interpretation: Taylor A. Rives, Ning Li, Donglin Yan, Charles S. Dietrich, Rachel W. Miller, Frederick R. Ueland, Jill M. Kolesar

Manuscript writing: All authors

Final approval of manuscript: All authors

Accountable for all aspects of the work: All authors

AUTHORS' DISCLOSURES OF POTENTIAL CONFLICTS OF INTEREST

The following represents disclosure information provided by authors of this manuscript. All relationships are considered compensated unless otherwise noted. Relationships are self-held unless noted. I = Immediate Family Member, Inst = My Institution. Relationships may not relate to the subject matter of this manuscript. For more information about ASCO's conflict of interest policy, please refer to www.asco.org/rwc or ascopubs.org/po/author-center.

Open Payments is a public database containing information reported by companies about payments made to US-licensed physicians (Open Payments).

Supported by National Cancer Institute at the National Institutes of Health, Division of Cancer Epidemiology and Genetics, grant number P30CA177558, B. Mark Evers and was supported by the Biostatistics and Bioinformatics Shared Resource, the Biospecimen Procurement and Translational Pathology Shared Resources, the Cancer Research Informatics Shared Resource and the Oncogenomics Shared Resource.

James Collard

Employment: University of Kentucky

Stock and Other Ownership Interests: dvax

Justine Pickarski

Employment: University of Kentucky

Travel, Accommodations, Expenses: University of Kentucky

Jill M. Kolesar

This author is a member of the JCO Precision Oncology Editorial Board. Journal policy recused the author from having any role in the peer review of this manuscript.

Stock and Other Ownership Interests: Helix Diagnostics, VesiCure Technologies

Consulting or Advisory Role: The Jackson Laboratory

Research Funding: ArtemiLife, Loxo/Lilly (Inst)

Patents, Royalties, Other Intellectual Property: Patent pending for a cell based therapy derived from human macrophages

Travel, Accommodations, Expenses: Caris Life Sciences

No other potential conflicts of interest were reported.
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