Association of Pathogenic Variants in Hereditary Cancer Genes With Multiple Diseases.

TitleAssociation of Pathogenic Variants in Hereditary Cancer Genes With Multiple Diseases.
Publication TypeJournal Article
Year of Publication2022
AuthorsZeng, C, Bastarache, LA, Tao, R, Venner, E, Hebbring, S, Andujar, JD, Bland, ST, Crosslin, DR, Pratap, S, Cooley, A, Pacheco, JA, Christensen, KD, Perez, E, Zawatsky, CLBlout, Witkowski, L, Zouk, H, Weng, C, Leppig, KA, Sleiman, PMA, Hakonarson, H, Williams, MS, Luo, Y, Jarvik, GP, Green, RC, Chung, WK, Gharavi, AG, Lennon, NJ, Rehm, HL, Gibbs, RA, Peterson, JF, Roden, DM, Wiesner, GL, Denny, JC
JournalJAMA Oncol
Date Published2022 Jun 01
KeywordsAcute Disease, Female, Gastritis, Genetic Predisposition to Disease, Germ-Line Mutation, Humans, Male, Neoplastic Syndromes, Hereditary, Pancreatitis

IMPORTANCE: Knowledge about the spectrum of diseases associated with hereditary cancer syndromes may improve disease diagnosis and management for patients and help to identify high-risk individuals.

OBJECTIVE: To identify phenotypes associated with hereditary cancer genes through a phenome-wide association study.

DESIGN, SETTING, AND PARTICIPANTS: This phenome-wide association study used health data from participants in 3 cohorts. The Electronic Medical Records and Genomics Sequencing (eMERGEseq) data set recruited predominantly healthy individuals from 10 US medical centers from July 16, 2016, through February 18, 2018, with a mean follow-up through electronic health records (EHRs) of 12.7 (7.4) years. The UK Biobank (UKB) cohort recruited participants from March 15, 2006, through August 1, 2010, with a mean (SD) follow-up of 12.4 (1.0) years. The Hereditary Cancer Registry (HCR) recruited patients undergoing clinical genetic testing at Vanderbilt University Medical Center from May 1, 2012, through December 31, 2019, with a mean (SD) follow-up through EHRs of 8.8 (6.5) years.

EXPOSURES: Germline variants in 23 hereditary cancer genes. Pathogenic and likely pathogenic variants for each gene were aggregated for association analyses.

MAIN OUTCOMES AND MEASURES: Phenotypes in the eMERGEseq and HCR cohorts were derived from the linked EHRs. Phenotypes in UKB were from multiple sources of health-related data.

RESULTS: A total of 214 020 participants were identified, including 23 544 in eMERGEseq cohort (mean [SD] age, 47.8 [23.7] years; 12 611 women [53.6%]), 187 234 in the UKB cohort (mean [SD] age, 56.7 [8.1] years; 104 055 [55.6%] women), and 3242 in the HCR cohort (mean [SD] age, 52.5 [15.5] years; 2851 [87.9%] women). All 38 established gene-cancer associations were replicated, and 19 new associations were identified. These included the following 7 associations with neoplasms: CHEK2 with leukemia (odds ratio [OR], 3.81 [95% CI, 2.64-5.48]) and plasma cell neoplasms (OR, 3.12 [95% CI, 1.84-5.28]), ATM with gastric cancer (OR, 4.27 [95% CI, 2.35-7.44]) and pancreatic cancer (OR, 4.44 [95% CI, 2.66-7.40]), MUTYH (biallelic) with kidney cancer (OR, 32.28 [95% CI, 6.40-162.73]), MSH6 with bladder cancer (OR, 5.63 [95% CI, 2.75-11.49]), and APC with benign liver/intrahepatic bile duct tumors (OR, 52.01 [95% CI, 14.29-189.29]). The remaining 12 associations with nonneoplastic diseases included BRCA1/2 with ovarian cysts (OR, 3.15 [95% CI, 2.22-4.46] and 3.12 [95% CI, 2.36-4.12], respectively), MEN1 with acute pancreatitis (OR, 33.45 [95% CI, 9.25-121.02]), APC with gastritis and duodenitis (OR, 4.66 [95% CI, 2.61-8.33]), and PTEN with chronic gastritis (OR, 15.68 [95% CI, 6.01-40.92]).

CONCLUSIONS AND RELEVANCE: The findings of this genetic association study analyzing the EHRs of 3 large cohorts suggest that these new phenotypes associated with hereditary cancer genes may facilitate early detection and better management of cancers. This study highlights the potential benefits of using EHR data in genomic medicine.

Alternate JournalJAMA Oncol
PubMed ID35446370
PubMed Central IDPMC9026237
Grant ListR01 LM010685 / LM / NLM NIH HHS / United States
T32 AI007281 / AI / NIAID NIH HHS / United States
MC_QA137853 / MRC_ / Medical Research Council / United Kingdom
MC_PC_17228 / MRC_ / Medical Research Council / United Kingdom
U01 HG008676 / HG / NHGRI NIH HHS / United States