Whole genome sequence analysis of pulmonary function and COPD in 19,996 multi-ethnic participants

Xutong Zhao, Dandi Qiao, Chaojie Yang, Silva Kasela, Wonji Kim, Yanlin Ma, Nick Shrine, Chiara Batini, Tamar Sofer, Sarah A. Gagliano Taliun, Phuwanat Sakornsakolpat, Pallavi P. Balte, Dmitry Prokopenko, Bing Yu, Leslie A. Lange, Josée Dupuis, Brian E. Cade, Jiwon Lee, Sina A. Gharib, Michelle Daya, Cecelia A. Laurie, Ingo Ruczinski, L. Adrienne Cupples, Laura R. Loehr, Traci M. Bartz, Alanna C. Morrison, Bruce M. Psaty, Ramachandran S. Vasan, James G. Wilson, Kent D. Taylor, Peter Durda, W. Craig Johnson, Elaine Cornell, Xiuqing Guo, Yongmei Liu, Russell P. Tracy, Kristin G. Ardlie, François Aguet, David J. VanDenBerg, George J. Papanicolaou, Jerome I. Rotter, Kathleen C. Barnes, Deepti Jain, Deborah A. Nickerson, Donna M. Muzny, Ginger A. Metcalf, Harshavardhan Doddapaneni, Shannon Dugan-Perez, Namrata Gupta, Stacey Gabriel, Stephen S. Rich, George T. O’Connor, Susan Redline, Robert M. Reed, Cathy C. Laurie, Martha L. Daviglus, Liana K. Preudhomme, Kristin M. Burkart, Robert C. Kaplan, Louise V. Wain, Martin D. Tobin, Stephanie J. London, Tuuli Lappalainen, Elizabeth C. Oelsner, Goncalo R. Abecasis, Edwin K. Silverman, R. Graham Barr, Michael H. Cho () and Ani Manichaikul ()
Additional contact information
Xutong Zhao: University of Michigan
Dandi Qiao: Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School
Chaojie Yang: University of Virginia
Silva Kasela: New York Genome Center
Wonji Kim: Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School
Yanlin Ma: University of Virginia
Nick Shrine: University of Leicester
Chiara Batini: University of Leicester
Tamar Sofer: Department of Medicine, Harvard Medical School
Sarah A. Gagliano Taliun: University of Michigan
Phuwanat Sakornsakolpat: Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School
Pallavi P. Balte: Department of Medicine, Columbia University Medical Center
Dmitry Prokopenko: Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School
Bing Yu: Department of Epidemiology, Human Genetics & Environmental Sciences, UTHealth School of Public Health
Leslie A. Lange: Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado School of Medicine Anschutz Medical Campus
Josée Dupuis: Boston University School of Public Health
Brian E. Cade: Department of Medicine, Harvard Medical School
Jiwon Lee: Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital
Sina A. Gharib: University of Washington
Michelle Daya: Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado School of Medicine Anschutz Medical Campus
Cecelia A. Laurie: University of Washington
Ingo Ruczinski: Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health
L. Adrienne Cupples: Boston University School of Public Health
Laura R. Loehr: Department of Medicine, UNC School of Medicine
Traci M. Bartz: University of Washington
Alanna C. Morrison: The University of Texas Health Science Center at Houston
Bruce M. Psaty: University of Washington
Ramachandran S. Vasan: Boston University and the National Heart Lung and Blood Institute’s Framingham Heart Study
James G. Wilson: University of Mississippi Medical Center
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
Peter Durda: University of Vermont
W. Craig Johnson: University of Washington
Elaine Cornell: University of Vermont
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
Yongmei Liu: Duke University Medical Center
Russell P. Tracy: University of Vermont
Kristin G. Ardlie: Broad Institute of MIT and Harvard
François Aguet: Broad Institute of MIT and Harvard
David J. VanDenBerg: University of Southern California
George J. Papanicolaou: Division of Cardiovascular Sciences, National Heart, Lung, and Blood Institute, National Institutes of Health
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
Kathleen C. Barnes: Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado School of Medicine Anschutz Medical Campus
Deepti Jain: University of Washington
Deborah A. Nickerson: University of Washington
Donna M. Muzny: The Human Genome Sequencing Center, Baylor College of Medicine
Ginger A. Metcalf: The Human Genome Sequencing Center, Baylor College of Medicine
Harshavardhan Doddapaneni: The Human Genome Sequencing Center, Baylor College of Medicine
Shannon Dugan-Perez: The Human Genome Sequencing Center, Baylor College of Medicine
Namrata Gupta: Broad Institute of MIT and Harvard
Stacey Gabriel: Broad Institute of MIT and Harvard
Stephen S. Rich: University of Virginia
George T. O’Connor: Boston University School Of Medicine, Pulmonary Center
Susan Redline: Department of Medicine, Harvard Medical School
Robert M. Reed: University of Maryland School of Medicine
Cathy C. Laurie: University of Washington
Martha L. Daviglus: University of Illinois at Chicago
Liana K. Preudhomme: University of Miami
Kristin M. Burkart: Department of Medicine, Columbia University Medical Center
Robert C. Kaplan: Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx
Louise V. Wain: University of Leicester
Martin D. Tobin: University of Leicester
Stephanie J. London: Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services
Tuuli Lappalainen: New York Genome Center
Elizabeth C. Oelsner: Department of Medicine, Columbia University Medical Center
Goncalo R. Abecasis: University of Michigan
Edwin K. Silverman: Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School
R. Graham Barr: Department of Medicine, Columbia University Medical Center
Michael H. Cho: Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School
Ani Manichaikul: University of Virginia

Nature Communications, 2020, vol. 11, issue 1, 1-12

Abstract: 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.

Date: 2020
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DOI: 10.1038/s41467-020-18334-7

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