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Selvaraj MS, Li X, Li Z, Pampana A, Zhang DY, Park J, Aslibekyan S, Bis JC, Brody JA, Cade BE, Chuang LM, Chung RH, Curran JE, de Las Fuentes L, de Vries PS, Duggirala R, Freedman BI, Graff M, Guo X, Heard-Costa N, Hidalgo B, Hwu CM, Irvin MR, Kelly TN, Kral BG, Lange L, Li X, Lisa M, Lubitz SA, Manichaikul AW, Michael P, Montasser ME, Morrison AC, Naseri T, O'Connell JR, Palmer ND, Peyser PA, Reupena MS, Smith JA, Sun X, Taylor KD, Tracy RP, Tsai MY, Wang Z, Wang Y, Bao W, Wilkins JT, Yanek LR, Zhao W, Arnett DK, Blangero J, Boerwinkle E, Bowden DW, Chen YDI, Correa A, Cupples LA, Dutcher SK, Ellinor PT, Fornage M, Gabriel S, Germer S, Gibbs R, He J, Kaplan RC, Kardia SLR, Kim R, Kooperberg C, Loos RJF, Viaud-Martinez KA, Mathias RA, McGarvey ST, Mitchell BD, Nickerson D, North KE, Psaty BM, Redline S, Reiner AP, Vasan RS, Rich SS, Willer C, Rotter JI, Rader DJ, Lin X, Peloso GM, Natarajan P. Whole genome sequence analysis of blood lipid levels in >66,000 individuals. Nat Commun 2022; 13:5995. [PMID: 36220816 PMCID: PMC9553944 DOI: 10.1038/s41467-022-33510-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 09/21/2022] [Indexed: 01/05/2023] Open
Abstract
Blood lipids are heritable modifiable causal factors for coronary artery disease. Despite well-described monogenic and polygenic bases of dyslipidemia, limitations remain in discovery of lipid-associated alleles using whole genome sequencing (WGS), partly due to limited sample sizes, ancestral diversity, and interpretation of clinical significance. Among 66,329 ancestrally diverse (56% non-European) participants, we associate 428M variants from deep-coverage WGS with lipid levels; ~400M variants were not assessed in prior lipids genetic analyses. We find multiple lipid-related genes strongly associated with blood lipids through analysis of common and rare coding variants. We discover several associated rare non-coding variants, largely at Mendelian lipid genes. Notably, we observe rare LDLR intronic variants associated with markedly increased LDL-C, similar to rare LDLR exonic variants. In conclusion, we conducted a systematic whole genome scan for blood lipids expanding the alleles linked to lipids for multiple ancestries and characterize a clinically-relevant rare non-coding variant model for lipids.
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Affiliation(s)
- Margaret Sunitha Selvaraj
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, 02114, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Xihao Li
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Zilin Li
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Akhil Pampana
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - David Y Zhang
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Joseph Park
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Stella Aslibekyan
- Department of Epidemiology, University of Alabama at Birmingham School of Public Health, Birmingham, AL, USA
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Brian E Cade
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Lee-Ming Chuang
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Ren-Hua Chung
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, 350, Taiwan
| | - Joanne E Curran
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, 78520, USA
| | - Lisa de Las Fuentes
- Department of Medicine, Cardiovascular Division, Washington University School of Medicine, St. Louis, MO, USA
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, USA
| | - Paul S de Vries
- 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, USA
| | - Ravindranath Duggirala
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, 78520, USA
| | - Barry I Freedman
- Department of Internal Medicine, Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Mariaelisa Graff
- Department of Epidemiology, UNC Chapel Hill, Chapel Hill, NC, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Nancy Heard-Costa
- Department of Neurology, Boston university School of Medicine, Boston, MA, USA
| | - Bertha Hidalgo
- Department of Epidemiology, University of Alabama at Birmingham School of Public Health, Birmingham, AL, USA
| | - Chii-Min Hwu
- Section of Endocrinology and Metabolism, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Marguerite R Irvin
- Department of Epidemiology, University of Alabama at Birmingham School of Public Health, Birmingham, AL, USA
| | - Tanika N Kelly
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, 70112, USA
- Tulane University Translational Science Institute, New Orleans, LA, 70112, USA
| | - Brian G Kral
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Leslie Lange
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Xiaohui Li
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Martin Lisa
- Department of Medicine, George Washington University, Washingron, DC, USA
| | - Steven A Lubitz
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, 02114, USA
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, 02124, USA
| | - Ani W Manichaikul
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Preuss Michael
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - May E Montasser
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, 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, USA
| | - Take Naseri
- Ministry of Health, Government of Samoa, Samoa, USA
| | - Jeffrey R O'Connell
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Nicholette D Palmer
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Patricia A Peyser
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, 48109, USA
| | | | - Jennifer A Smith
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Xiao Sun
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, 70112, USA
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Russell P Tracy
- Departments of Pathology & Laboratory Medicine and Biochemistry, Larner College of Medicine at the University of Vermont, Colchester, VT, USA
| | - Michael Y Tsai
- Department of Laboratory Medicine and Pathology, University of Minneosta, Minneapolis, MN, USA
| | - Zhe Wang
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yuxuan Wang
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
| | - Wei Bao
- Institute of Public Health, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - John T Wilkins
- Department of Medicine (Cardiology) and Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Lisa R Yanek
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Wei Zhao
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Donna K Arnett
- Dean's Office, University of Kentucky College of Public Health, Lexington, KY, USA
| | - John Blangero
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, 78520, USA
| | - Eric Boerwinkle
- 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, USA
| | - Donald W Bowden
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Yii-Der Ida Chen
- Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Adolfo Correa
- Department of Population Health Science, University of Mississippi Medical Center, Jackson, MS, USA
| | - L Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
| | - Susan K Dutcher
- The McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63108, USA
| | - Patrick T Ellinor
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, 02114, USA
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, 02124, USA
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 7722, USA
| | | | - Soren Germer
- New York Genome Center, New York, NY, 10013, USA
| | - Richard Gibbs
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, 77030, USA
| | - Jiang He
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, 70112, USA
- Tulane University Translational Science Institute, New Orleans, LA, 70112, USA
| | - Robert C Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Sharon L R Kardia
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Ryan Kim
- Psomagen, Inc. (formerly Macrogen USA), Rockville, MD, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- NNF Center for Basic Metabolic Research, University of Copenhagen, Cophenhagen, Denmark
| | | | - Rasika A Mathias
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Stephen T McGarvey
- Department of Epidemiology, International Health Institute, Brown University, Providence, RI, USA
| | - Braxton D Mitchell
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Geriatrics Research and Education Clinical Center, Baltimore Veterans Administration Medical Center, Baltimore, MD, USA
| | - Deborah Nickerson
- University of Washington, Department of Genome Sciences, Seattle, WA, 98195, USA
| | - Kari E North
- Department of Epidemiology, UNC Chapel Hill, Chapel Hill, NC, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Health Systems and Population Health, University of Washington, Seattle, WA, USA
| | - Susan Redline
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Alexander P Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Ramachandran S Vasan
- Sections of Preventive medicine and Epidemiology, Cardiovascular medicine, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA
- Framingham Heart Study, Framingham, MA, USA
| | - Stephen S Rich
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Cristen Willer
- University of Michigan, Internal Medicine, Ann Arbor, MI, 48109, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Daniel J Rader
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Xihong Lin
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
- Department of Statistics, Harvard University, Cambridge, MA, 02138, USA
| | - Gina M Peloso
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA.
| | - Pradeep Natarajan
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, 02114, USA.
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA.
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