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Zhao X, Qiao D, Yang C, Kasela S, Kim W, Ma Y, Shrine N, Batini C, Sofer T, Taliun SAG, Sakornsakolpat P, Balte PP, Prokopenko D, Yu B, Lange LA, Dupuis J, Cade BE, Lee J, Gharib SA, Daya M, Laurie CA, Ruczinski I, Cupples LA, Loehr LR, Bartz TM, Morrison AC, Psaty BM, Vasan RS, Wilson JG, Taylor KD, Durda P, Johnson WC, Cornell E, Guo X, Liu Y, Tracy RP, Ardlie KG, Aguet F, VanDenBerg DJ, Papanicolaou GJ, Rotter JI, Barnes KC, Jain D, Nickerson DA, Muzny DM, Metcalf GA, Doddapaneni H, Dugan-Perez S, Gupta N, Gabriel S, Rich SS, O'Connor GT, Redline S, Reed RM, Laurie CC, Daviglus ML, Preudhomme LK, Burkart KM, Kaplan RC, Wain LV, Tobin MD, London SJ, Lappalainen T, Oelsner EC, Abecasis GR, Silverman EK, Barr RG, Cho MH, Manichaikul A. Whole genome sequence analysis of pulmonary function and COPD in 19,996 multi-ethnic participants. Nat Commun 2020; 11:5182. [PMID: 33057025 PMCID: PMC7598941 DOI: 10.1038/s41467-020-18334-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 08/19/2020] [Indexed: 12/14/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD), diagnosed by reduced lung function, is a leading cause of morbidity and mortality. We performed whole genome sequence (WGS) analysis of lung function and COPD in a multi-ethnic sample of 11,497 participants from population- and family-based studies, and 8499 individuals from COPD-enriched studies in the NHLBI Trans-Omics for Precision Medicine (TOPMed) Program. We identify at genome-wide significance 10 known GWAS loci and 22 distinct, previously unreported loci, including two common variant signals from stratified analysis of African Americans. Four novel common variants within the regions of PIAS1, RGN (two variants) and FTO show evidence of replication in the UK Biobank (European ancestry n ~ 320,000), while colocalization analyses leveraging multi-omic data from GTEx and TOPMed identify potential molecular mechanisms underlying four of the 22 novel loci. Our study demonstrates the value of performing WGS analyses and multi-omic follow-up in cohorts of diverse ancestry.
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Affiliation(s)
- Xutong Zhao
- Center for Statistical Genetics, and Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Dandi Qiao
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Chaojie Yang
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Silva Kasela
- New York Genome Center, New York, NY, 10013, USA
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
| | - Wonji Kim
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Yanlin Ma
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Nick Shrine
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, LE1 7RH, United Kingdom
| | - Chiara Batini
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, LE1 7RH, United Kingdom
| | - Tamar Sofer
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Sarah A Gagliano Taliun
- Center for Statistical Genetics, and Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Phuwanat Sakornsakolpat
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Pallavi P Balte
- Department of Medicine, Columbia University Medical Center, New York, NY, 10032, USA
| | - Dmitry Prokopenko
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Bing Yu
- Department of Epidemiology, Human Genetics & Environmental Sciences, UTHealth School of Public Health, Houston, TX, 77030, USA
| | - Leslie A Lange
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado School of Medicine Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
| | - Brian E Cade
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Jiwon Lee
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Sina A Gharib
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, WA, 98109, USA
| | - Michelle Daya
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado School of Medicine Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Cecelia A Laurie
- Department of Biostatistics, University of Washington, Seattle, WA, 98195, USA
| | - Ingo Ruczinski
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - L Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
- Boston University and the National Heart Lung and Blood Institute's Framingham Heart Study, Framingham, MA, 01702, USA
| | - Laura R Loehr
- Department of Medicine, UNC School of Medicine, Chapel Hill, NC, 27599, USA
| | - Traci M Bartz
- Department of Biostatistics, University of Washington, Seattle, WA, 98195, USA
| | - Alanna C Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, and Health Services, University of Washington, Seattle, WA, 98101, USA
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, 98101, USA
| | - Ramachandran S Vasan
- Boston University and the National Heart Lung and Blood Institute's Framingham Heart Study, Framingham, MA, 01702, USA
- Department of Preventive Medicine and Epidemiology, Boston University School of Medicine and Public Health, Boston, MA, 02118, USA
| | - James G Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS, 39216, USA
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, The Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, 90502, USA
| | - Peter Durda
- Department of Pathology and Laboratory Medicine, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT, 05405, USA
| | - W Craig Johnson
- Department of Biostatistics, University of Washington, Seattle, WA, 98195, USA
| | - Elaine Cornell
- Department of Pathology and Laboratory Medicine, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT, 05405, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, The Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, 90502, USA
| | - Yongmei Liu
- Department of Medicine, Division of Cardiology, Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, 27701, USA
| | - Russell P Tracy
- Department of Pathology and Laboratory Medicine, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT, 05405, USA
| | | | - François Aguet
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - David J VanDenBerg
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - George J Papanicolaou
- Division of Cardiovascular Sciences, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, The Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, 90502, USA
| | - Kathleen C Barnes
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado School of Medicine Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Deepti Jain
- Department of Biostatistics, University of Washington, Seattle, WA, 98195, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Donna M Muzny
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ginger A Metcalf
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | | | - Shannon Dugan-Perez
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Namrata Gupta
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Stacey Gabriel
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA
| | - George T O'Connor
- Boston University School Of Medicine, Pulmonary Center, Boston, MA, 02118, USA
| | - Susan Redline
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Division of Pulmonary, Critical Care, and Sleep Medicine, Beth Israel Deaconess Medical Center, Boston, MA, 02215, USA
| | - Robert M Reed
- Division of Pulmonary and Critical Care Medicine, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Cathy C Laurie
- Department of Biostatistics, University of Washington, Seattle, WA, 98195, USA
| | - Martha L Daviglus
- Institute for Minority Health Research, University of Illinois at Chicago, Chicago, IL, 60612, USA
| | | | - Kristin M Burkart
- Department of Medicine, Columbia University Medical Center, New York, NY, 10032, USA
| | - Robert C Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York, NY, 10461, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Louise V Wain
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, LE1 7RH, United Kingdom
- National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, LE3 9QP, UK
| | - Martin D Tobin
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, LE1 7RH, United Kingdom
- National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, LE3 9QP, UK
| | - Stephanie J London
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Durham, NC, 27709, USA
| | - Tuuli Lappalainen
- New York Genome Center, New York, NY, 10013, USA
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
| | - Elizabeth C Oelsner
- Department of Medicine, Columbia University Medical Center, New York, NY, 10032, USA
| | - Goncalo R Abecasis
- Center for Statistical Genetics, and Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - R Graham Barr
- Department of Medicine, Columbia University Medical Center, New York, NY, 10032, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA.
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