Mutation Detection in Patients With Advanced Cancer by Universal Sequencing of Cancer-Related Genes in Tumor and Normal DNA vs Guideline-Based Germline Testing

Abstract

Importance: Guidelines for cancer genetic testing based on family history may miss clinically actionable genetic changes with established implications for cancer screening or prevention.

Objective: To determine the proportion and potential clinical implications of inherited variants detected using simultaneous sequencing of the tumor and normal tissue ("tumor-normal sequencing") compared with genetic test results based on current guidelines.

Design, setting, and participants: From January 2014 until May 2016 at Memorial Sloan Kettering Cancer Center, 10 336 patients consented to tumor DNA sequencing. Since May 2015, 1040 of these patients with advanced cancer were referred by their oncologists for germline analysis of 76 cancer predisposition genes. Patients with clinically actionable inherited mutations whose genetic test results would not have been predicted by published decision rules were identified. Follow-up for potential clinical implications of mutation detection was through May 2017.

Exposure: Tumor and germline sequencing compared with the predicted yield of targeted germline sequencing based on clinical guidelines.

Main outcomes and measures: Proportion of clinically actionable germline mutations detected by universal tumor-normal sequencing that would not have been detected by guideline-directed testing.

Results: Of 1040 patients, the median age was 58 years (interquartile range, 50.5-66 years), 65.3% were male, and 81.3% had stage IV disease at the time of genomic analysis, with prostate, renal, pancreatic, breast, and colon cancer as the most common diagnoses. Of the 1040 patients, 182 (17.5%; 95% CI, 15.3%-19.9%) had clinically actionable mutations conferring cancer susceptibility, including 149 with moderate- to high-penetrance mutations; 101 patients tested (9.7%; 95% CI, 8.1%-11.7%) would not have had these mutations detected using clinical guidelines, including 65 with moderate- to high-penetrance mutations. Frequency of inherited mutations was related to case mix, stage, and founder mutations. Germline findings led to discussion or initiation of change to targeted therapy in 38 patients tested (3.7%) and predictive testing in the families of 13 individuals (1.3%), including 6 for whom genetic evaluation would not have been initiated by guideline-based testing.

Conclusions and relevance: In this referral population with selected advanced cancers, universal sequencing of a broad panel of cancer-related genes in paired germline and tumor DNA samples was associated with increased detection of individuals with potentially clinically significant heritable mutations over the predicted yield of targeted germline testing based on current clinical guidelines. Knowledge of these additional mutations can help guide therapeutic and preventive interventions, but whether all of these interventions would improve outcomes for patients with cancer or their family members requires further study.

Trial registration: clinicaltrials.gov Identifier: NCT01775072.

Conflict of interest statement

Conflict of Interest Disclosures: All authors have completed and submitted the ICMJE Form for Disclosure of Potential Conflicts of Interest. Ms Kemel reported prior employment at Bioreference Laboratories. Dr Lowery reported serving on advisory boards for Agios Pharmaceuticals and Celgene. Dr Sawyers reporting serving on the board of directors for Novartis. Dr Dickler reported serving on advisory boards for Genentech/Roche, Novartis, Pfizer, Puma Biotech, AstraZeneca, and TapImmune. Dr Saltz reported receiving a grant from Taiho Pharmaceutical. Dr Scher reported serving as a consultant to Astellas, BIND Therapeutics, Clovis Oncology, Ferring Pharmaceuticals, Janssen Research and Development, Medivation, Merck, Roche, Sanofi Aventis, Takeda Millennium, and WIRB-Copernicus Group; receiving support to the Memorial Sloan Kettering Cancer Center from Medivation, Janssen, Illumina, and Innocrin Pharmaceuticals; and serving on the board of directors for Asterias Biotherapeutics. Dr Solit reported serving as a consultant to Pfizer and Loxo Oncology. Dr Hyman reported serving as a consultant to Chugai, CytomX, Boehringer Ingelheim, and Atara Biotherapeutics; and receiving grants from AstraZeneca, Puma Biotechnology, and Loxo Oncology. Dr Ladanyi reported receiving personal fees from Boehringer Ingelheim and AstraZeneca through the National Comprehensive Cancer Network; and a receiving a grant from Loxo Oncology. No other disclosures were reported.

Figures

Figure. Clinical Actionability, Concordance With Family History and Phenotype, Penetrance, and Founder Mutations in 1040 Patients Undergoing Sequencing of Germline and Tumor DNA

Representation of the 1040 cases that carried clinically actionable pathogenic or presumed pathogenic variants, comprising 182 cases broken into subsets of no incremental cases (in which mutations would have been detected using genetic testing guidelines based on phenotype and family history) and incremental cases (in which mutations would not have been detected using guideline-based approaches). The incremental cases are categorized by high-, moderate-, or low-penetrance mutations. Numbers in parentheses indicate the numbers of patients in that category without Ashkenazi Jewish or European founder mutations.