TY - JOUR
T1 - Association of Pathogenic Variants in Hereditary Cancer Genes With Multiple Diseases
AU - Zeng, Chenjie
AU - Bastarache, Lisa A.
AU - Tao, Ran
AU - Venner, Eric
AU - Hebbring, Scott
AU - Andujar, Justin D.
AU - Bland, Sarah T.
AU - Crosslin, David R.
AU - Pratap, Siddharth
AU - Cooley, Ayorinde
AU - Pacheco, Jennifer A.
AU - Christensen, Kurt D.
AU - Perez, Emma
AU - Blout Zawatsky, Carrie L.
AU - Witkowski, Leora
AU - Zouk, Hana
AU - Weng, Chunhua
AU - Leppig, Kathleen A.
AU - Sleiman, Patrick M.A.
AU - Hakonarson, Hakon
AU - Williams, Marc S.
AU - Luo, Yuan
AU - Jarvik, Gail P.
AU - Green, Robert C.
AU - Chung, Wendy K.
AU - Gharavi, Ali G.
AU - Lennon, Niall J.
AU - Rehm, Heidi L.
AU - Gibbs, Richard A.
AU - Peterson, Josh F.
AU - Roden, Dan M.
AU - Wiesner, Georgia L.
AU - Denny, Joshua C.
N1 - Publisher Copyright:
© 2022 American Medical Association.
PY - 2022/6
Y1 - 2022/6
N2 - 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 214020 participants were identified, including 23544 in eMERGEseq cohort (mean [SD] age, 47.8 [23.7] years; 12611 women [53.6%]), 187234 in the UKB cohort (mean [SD] age, 56.7 [8.1] years; 104055 [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.
AB - 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 214020 participants were identified, including 23544 in eMERGEseq cohort (mean [SD] age, 47.8 [23.7] years; 12611 women [53.6%]), 187234 in the UKB cohort (mean [SD] age, 56.7 [8.1] years; 104055 [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.
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U2 - 10.1001/jamaoncol.2022.0373
DO - 10.1001/jamaoncol.2022.0373
M3 - Article
C2 - 35446370
AN - SCOPUS:85129380234
SN - 2374-2437
VL - 8
SP - 835
EP - 844
JO - JAMA Oncology
JF - JAMA Oncology
IS - 6
ER -
