Abstract
Plasma concentrations of total cholesterol, low-density lipoprotein cholesterol, high-density lipoprotein cholesterol and triglycerides are among the most important risk factors for coronary artery disease (CAD) and are targets for therapeutic intervention. We screened the genome for common variants associated with plasma lipids in >100,000 individuals of European ancestry. Here we report 95 significantly associated loci (P < 5 × 10−8), with 59 showing genome-wide significant association with lipid traits for the first time. The newly reported associations include single nucleotide polymorphisms (SNPs) near known lipid regulators (for example, CYP7A1, NPC1L1 and SCARB1) as well as in scores of loci not previously implicated in lipoprotein metabolism. The 95 loci contribute not only to normal variation in lipid traits but also to extreme lipid phenotypes and have an impact on lipid traits in three non-European populations (East Asians, South Asians and African Americans). Our results identify several novel loci associated with plasma lipids that are also associated with CAD. Finally, we validated three of the novel genes—GALNT2, PPP1R3B and TTC39B—with experiments in mouse models. Taken together, our findings provide the foundation to develop a broader biological understanding of lipoprotein metabolism and to identify new therapeutic opportunities for the prevention of CAD.
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Acknowledgements
We wish to dedicate this paper to the memory of Dr Leena Peltonen, who passed away on 11 March 2010. A full listing of acknowledgements is provided in Supplementary Information.
Author information
Author notes
- Tanya M. Teslovich
- , Kiran Musunuru
- , L. Adrienne Cupples
- , Manjinder S. Sandhu
- , Paul M Ridker
- , Daniel J. Rader
- , Cornelia M. van Duijn
- , Gonçalo R. Abecasis
- , Michael Boehnke
- & Sekar Kathiresan
These authors contributed equally to this work.
- Leena Peltonen
Deceased.
Affiliations
Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, Michigan 48109, USA.
- Tanya M. Teslovich
- , Cristen J. Willer
- , Heather M. Stringham
- , Gonçalo R. Abecasis
- & Michael Boehnke
Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.
- Kiran Musunuru
- , James P. Pirruccello
- , Benjamin F. Voight
- , David Altshuler
- & Sekar Kathiresan
Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.
- Kiran Musunuru
- & Sekar Kathiresan
Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, USA.
- Kiran Musunuru
- , Daniel I. Chasman
- , Robert Y. L. Zee
- , Christopher J. O’Donnell
- , David Altshuler
- , Paul M Ridker
- & Sekar Kathiresan
Broad Institute, Cambridge, Massachusetts 02142, USA.
- Kiran Musunuru
- , James P. Pirruccello
- , Benjamin F. Voight
- , Candace Guiducci
- , Elena Gonzalez
- , Kenechi G. Ejebe
- , Gabriel Crawford
- , Noel P. Burtt
- , David Altshuler
- , Stacey B. Gabriel
- & Sekar Kathiresan
Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA.
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- & James P. Pirruccello
Icelandic Heart Association, Heart Preventive Clinic and Research Institute, 201 Kopavogur, Iceland.
- Albert V. Smith
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University of Iceland, 101 Reykjavik, Iceland.
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Cardiovascular Institute, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA.
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- , Muredach P. Reilly
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Institute for Translational Medicine and Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA.
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Department of Vascular Medicine, Academic Medical Centre at the University of Amsterdam, 1105 AZ Amsterdam, The Netherlands.
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Interdisciplinary Program in Bioinformatics, College of Natural Sciences, Seoul National University, Seoul 151-742, Republic of Korea.
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Department of Statistics, College of Natural Sciences, Seoul National University, Seoul 151-742, Republic of Korea.
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Department of Statistics, Sookmyung Women’s University, Seoul 140-742, Republic of Korea.
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Centre for Molecular Epidemiology, National University of Singapore, Singapore 117597, Republic of Singapore.
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Genome Institute of Singapore, Singapore 138672, Republic of Singapore.
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Medstar Research Institute, Baltimore, Maryland 21218, USA.
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Clinical Pharmacology and Barts and The London Genome Centre, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK.
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Sage Bionetworks, Seattle, Washington 98109, USA.
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Division of Community Health Sciences, St George’s University of London, London SW17 0RE, UK.
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Contributions
T.M.T., K.M., A.V.S., A.C.E., I.M.S., M.K. and J.P.P. carried out the primary data analyses and/or experimental work. All other authors contributed to additional analyses. L.A.C., M.S.S., P.M.R., D.J.R., C.M.v.D., L.P., G.R.A., M.B. and S.K. conceived, designed, and supervised the study. K.M. wrote the manuscript.
Competing interests
Competing interests: D.M.W., K.S. and V.M. are full-time employees of GlaxoSmithKline. M.S.S. has received research funding from GlaxoSmithKline. P.V. and G.W. received grant money from GlaxoSmithKline to fund the CoLaus study. G.T., K.S., U.T. and H.H. are full-time employees of deCODE genetics. The other authors declare no competing financial interests.
Corresponding author
Correspondence to Sekar Kathiresan.
Supplementary information
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Supplementary Information
This file contains Supplementary Methods, References, Supplementary Figures 1-3 with legends, Supplementary Tables 1-19 and a full list of Acknowledgments.
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