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Buchanan AH, Manickam K, Meyer MN, Wagner JK, Hallquist MLG, Williams JL, Rahm AK, Williams MS, Chen ZME, Shah CK, Garg TK, Lazzeri AL, Schwartz MLB, Lindbuchler DAM, Fan AL, Leeming R, Servano PO, Smith AL, Vogel VG, Abul-Husn NS, Dewey FE, Lebo MS, Mason-Suares HM, Ritchie MD, Davis FD, Carey DJ, Feinberg DT, Faucett WA, Ledbetter DH, Murray MF. Correction to: Early cancer diagnoses through BRCA1/2 screening of unselected adult biobank participants. Genet Med 2021; 23:2470. [PMID: 34646007 PMCID: PMC9119243 DOI: 10.1038/s41436-021-01304-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Adam H Buchanan
- Geisinger Health System, Danville, PA, USA. .,Genomic Medicine Institute, Geisinger Health System, Danville, PA, USA.
| | - Kandamurugu Manickam
- Geisinger Health System, Danville, PA, USA.,Genomic Medicine Institute, Geisinger Health System, Danville, PA, USA
| | - Michelle N Meyer
- Geisinger Health System, Danville, PA, USA.,Center for Translational Bioethics and Health Care Policy, Geisinger Health System, Danville, PA, USA
| | - Jennifer K Wagner
- Geisinger Health System, Danville, PA, USA.,Center for Translational Bioethics and Health Care Policy, Geisinger Health System, Danville, PA, USA
| | - Miranda L G Hallquist
- Geisinger Health System, Danville, PA, USA.,Genomic Medicine Institute, Geisinger Health System, Danville, PA, USA
| | - Janet L Williams
- Geisinger Health System, Danville, PA, USA.,Genomic Medicine Institute, Geisinger Health System, Danville, PA, USA
| | - Alanna Kulchak Rahm
- Geisinger Health System, Danville, PA, USA.,Genomic Medicine Institute, Geisinger Health System, Danville, PA, USA
| | - Marc S Williams
- Geisinger Health System, Danville, PA, USA.,Genomic Medicine Institute, Geisinger Health System, Danville, PA, USA
| | - Zong-Ming E Chen
- Geisinger Health System, Danville, PA, USA.,Laboratory Medicine, Geisinger Health System, Danville, PA, USA
| | - Chaitali K Shah
- Geisinger Health System, Danville, PA, USA.,Radiology, Geisinger Health System, Danville, PA, USA
| | - Tullika K Garg
- Geisinger Health System, Danville, PA, USA.,Department of Urology, Geisinger Health System, Danville, PA, USA
| | - Amanda L Lazzeri
- Geisinger Health System, Danville, PA, USA.,Genomic Medicine Institute, Geisinger Health System, Danville, PA, USA
| | - Marci L B Schwartz
- Geisinger Health System, Danville, PA, USA.,Genomic Medicine Institute, Geisinger Health System, Danville, PA, USA
| | - D' Andra M Lindbuchler
- Geisinger Health System, Danville, PA, USA.,Genomic Medicine Institute, Geisinger Health System, Danville, PA, USA
| | - Audrey L Fan
- Geisinger Health System, Danville, PA, USA.,Genomic Medicine Institute, Geisinger Health System, Danville, PA, USA
| | - Rosemary Leeming
- Geisinger Health System, Danville, PA, USA.,General Surgery, Geisinger Health System, Danville, PA, USA
| | - Pedro O Servano
- Geisinger Health System, Danville, PA, USA.,Family Medicine, Geisinger Health System, Danville, PA, USA
| | - Ashlee L Smith
- Geisinger Health System, Danville, PA, USA.,Women's Health, Geisinger Health System, Danville, PA, USA
| | - Victor G Vogel
- Geisinger Health System, Danville, PA, USA.,Hematology & Oncology, Geisinger Health System, Danville, PA, USA
| | | | | | - Matthew S Lebo
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, MA, USA
| | - Heather M Mason-Suares
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, MA, USA
| | - Marylyn D Ritchie
- Geisinger Health System, Danville, PA, USA.,Biomedical and Translational Informatics, Geisinger Health System, Danville, PA, USA
| | - F Daniel Davis
- Geisinger Health System, Danville, PA, USA.,Center for Translational Bioethics and Health Care Policy, Geisinger Health System, Danville, PA, USA
| | - David J Carey
- Geisinger Health System, Danville, PA, USA.,Department of Molecular and Functional Genomics, Geisinger Health System, Danville, PA, USA
| | - David T Feinberg
- Geisinger Health System, Danville, PA, USA.,Office of the Chief Executive Officer, Geisinger Health System, Danville, PA, USA
| | - W Andrew Faucett
- Geisinger Health System, Danville, PA, USA.,Genomic Medicine Institute, Geisinger Health System, Danville, PA, USA
| | - David H Ledbetter
- Geisinger Health System, Danville, PA, USA.,Genomic Medicine Institute, Geisinger Health System, Danville, PA, USA
| | - Michael F Murray
- Geisinger Health System, Danville, PA, USA.,Genomic Medicine Institute, Geisinger Health System, Danville, PA, USA
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Manickam K, Buchanan AH, Schwartz MLB, Hallquist MLG, Williams JL, Rahm AK, Rocha H, Savatt JM, Evans AE, Butry LM, Lazzeri AL, Lindbuchler DM, Flansburg CN, Leeming R, Vogel VG, Lebo MS, Mason-Suares HM, Hoskinson DC, Abul-Husn NS, Dewey FE, Overton JD, Reid JG, Baras A, Willard HF, McCormick CZ, Krishnamurthy SB, Hartzel DN, Kost KA, Lavage DR, Sturm AC, Frisbie LR, Person TN, Metpally RP, Giovanni MA, Lowry LE, Leader JB, Ritchie MD, Carey DJ, Justice AE, Kirchner HL, Faucett WA, Williams MS, Ledbetter DH, Murray MF. Exome Sequencing-Based Screening for BRCA1/2 Expected Pathogenic Variants Among Adult Biobank Participants. JAMA Netw Open 2018; 1:e182140. [PMID: 30646163 PMCID: PMC6324494 DOI: 10.1001/jamanetworkopen.2018.2140] [Citation(s) in RCA: 140] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
IMPORTANCE Detection of disease-associated variants in the BRCA1 and BRCA2 (BRCA1/2) genes allows for cancer prevention and early diagnosis in high-risk individuals. OBJECTIVES To identify pathogenic and likely pathogenic (P/LP) BRCA1/2 variants in an unselected research cohort, and to characterize the features associated with P/LP variants. DESIGN, SETTING, AND PARTICIPANTS This is a cross-sectional study of adult volunteers (n = 50 726) who underwent exome sequencing at a single health care system (Geisinger Health System, Danville, Pennsylvania) from January 1, 2014, to March 1, 2016. Participants are part of the DiscovEHR cohort and were identified through the Geisinger MyCode Community Health Initiative. They consented to a research protocol that included sequencing and return of actionable test results. Clinical data from electronic health records and clinical visits were correlated with variants. Comparisons were made between those with (cases) and those without (controls) P/LP variants in BRCA1/2. MAIN OUTCOMES Prevalence of P/LP BRCA1/2 variants in cohort, proportion of variant carriers not previously ascertained through clinical testing, and personal and family history of relevant cancers among BRCA1/2 variant carriers and noncarriers. RESULTS Of the 50 726 health system patients who underwent exome sequencing, 50 459 (99.5%) had no expected pathogenic BRCA1/2 variants and 267 (0.5%) were BRCA1/2 carriers. Of the 267 cases (148 [55.4%] were women and 119 [44.6%] were men with a mean [range] age of 58.9 [23-90] years), 183 (68.5%) received clinically confirmed results in their electronic health record. Among the 267 participants with P/LP BRCA1/2 variants, 219 (82.0%) had no prior clinical testing, 95 (35.6%) had BRCA1 variants, and 172 (64.4%) had BRCA2 variants. Syndromic cancer diagnoses were present in 11 (47.8%) of the 23 deceased BRCA1/2 carriers and in 56 (20.9%) of all 267 BRCA1/2 carriers. Among women, 31 (20.9%) of 148 variant carriers had a personal history of breast cancer, compared with 1554 (5.2%) of 29 880 noncarriers (odds ratio [OR], 5.95; 95% CI, 3.88-9.13; P < .001). Ovarian cancer history was present in 15 (10.1%) of 148 variant carriers and in 195 (0.6%) of 29 880 variant noncarriers (OR, 18.30; 95% CI, 10.48-31.4; P < .001). Among 89 BRCA1/2 carriers without prior testing but with comprehensive personal and family history data, 44 (49.4%) did not meet published guidelines for clinical testing. CONCLUSIONS AND RELEVANCE This study found that compared with previous clinical care, exome sequencing-based screening identified 5 times as many individuals with P/LP BRCA1/2 variants. These findings suggest that genomic screening may identify BRCA1/2-associated cancer risk that might otherwise remain undetected within health care systems and may provide opportunities to reduce morbidity and mortality in patients.
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Affiliation(s)
- Kandamurugu Manickam
- Molecular and Human Genetics Department, Nationwide Children’s Hospital, Columbus, Ohio
- Genomic Medicine Institute, Geisinger, Danville, Pennsylvania
| | | | | | | | | | | | - Heather Rocha
- Genomic Medicine Institute, Geisinger, Danville, Pennsylvania
| | | | - Alyson E. Evans
- Genomic Medicine Institute, Geisinger, Danville, Pennsylvania
| | - Loren M. Butry
- Genomic Medicine Institute, Geisinger, Danville, Pennsylvania
| | | | | | | | | | - Victor G. Vogel
- Genomic Medicine Institute, Geisinger, Danville, Pennsylvania
| | - Matthew S. Lebo
- Laboratory for Molecular Medicine, Partners HealthCare, Cambridge, Massachusetts
| | | | - Derick C. Hoskinson
- Laboratory for Molecular Medicine, Partners HealthCare, Cambridge, Massachusetts
| | | | | | | | | | - Aris Baras
- Regeneron Genetics Center, Tarrytown, New York
| | | | | | | | | | - Korey A. Kost
- Genomic Medicine Institute, Geisinger, Danville, Pennsylvania
| | | | - Amy C. Sturm
- Genomic Medicine Institute, Geisinger, Danville, Pennsylvania
| | | | - T. Nate Person
- Genomic Medicine Institute, Geisinger, Danville, Pennsylvania
| | | | | | - Lacy E. Lowry
- Genomic Medicine Institute, Geisinger, Danville, Pennsylvania
| | | | - Marylyn D. Ritchie
- Genomic Medicine Institute, Geisinger, Danville, Pennsylvania
- Center for Translational Bioinformatics, University of Pennsylvania, Philadelphia
| | - David J. Carey
- Genomic Medicine Institute, Geisinger, Danville, Pennsylvania
| | - Anne E. Justice
- Genomic Medicine Institute, Geisinger, Danville, Pennsylvania
| | | | | | | | | | - Michael F. Murray
- Genomic Medicine Institute, Geisinger, Danville, Pennsylvania
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut
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Dewey FE, Murray MF, Overton JD, Habegger L, Leader JB, Fetterolf SN, O'Dushlaine C, Van Hout CV, Staples J, Gonzaga-Jauregui C, Metpally R, Pendergrass SA, Giovanni MA, Kirchner HL, Balasubramanian S, Abul-Husn NS, Hartzel DN, Lavage DR, Kost KA, Packer JS, Lopez AE, Penn J, Mukherjee S, Gosalia N, Kanagaraj M, Li AH, Mitnaul LJ, Adams LJ, Person TN, Praveen K, Marcketta A, Lebo MS, Austin-Tse CA, Mason-Suares HM, Bruse S, Mellis S, Phillips R, Stahl N, Murphy A, Economides A, Skelding KA, Still CD, Elmore JR, Borecki IB, Yancopoulos GD, Davis FD, Faucett WA, Gottesman O, Ritchie MD, Shuldiner AR, Reid JG, Ledbetter DH, Baras A, Carey DJ. Distribution and clinical impact of functional variants in 50,726 whole-exome sequences from the DiscovEHR study. Science 2017; 354:354/6319/aaf6814. [PMID: 28008009 DOI: 10.1126/science.aaf6814] [Citation(s) in RCA: 364] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 11/16/2016] [Indexed: 11/02/2022]
Abstract
The DiscovEHR collaboration between the Regeneron Genetics Center and Geisinger Health System couples high-throughput sequencing to an integrated health care system using longitudinal electronic health records (EHRs). We sequenced the exomes of 50,726 adult participants in the DiscovEHR study to identify ~4.2 million rare single-nucleotide variants and insertion/deletion events, of which ~176,000 are predicted to result in a loss of gene function. Linking these data to EHR-derived clinical phenotypes, we find clinical associations supporting therapeutic targets, including genes encoding drug targets for lipid lowering, and identify previously unidentified rare alleles associated with lipid levels and other blood level traits. About 3.5% of individuals harbor deleterious variants in 76 clinically actionable genes. The DiscovEHR data set provides a blueprint for large-scale precision medicine initiatives and genomics-guided therapeutic discovery.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Korey A Kost
- Geisinger Health System, Danville, PA 17822, USA
| | | | | | - John Penn
- Regeneron Genetics Center, Tarrytown, NY 10591, USA
| | | | | | | | | | | | | | | | | | | | - Matthew S Lebo
- Laboratory for Molecular Medicine, Cambridge, MA 02139, USA
| | | | | | | | - Scott Mellis
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | | | - Neil Stahl
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Aris Baras
- Regeneron Genetics Center, Tarrytown, NY 10591, USA
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