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Surakka I, Horikoshi M, Mägi R, Sarin AP, Mahajan A, Lagou V, Marullo L, Ferreira T, Miraglio B, Timonen S, Kettunen J, Pirinen M, Karjalainen J, Thorleifsson G, Hägg S, Hottenga JJ, Isaacs A, Ladenvall C, Beekman M, Esko T, Ried JS, Nelson CP, Willenborg C, Gustafsson S, Westra HJ, Blades M, de Craen AJM, de Geus EJ, Deelen J, Grallert H, Hamsten A, Havulinna AS, Hengstenberg C, Houwing-Duistermaat JJ, Hyppönen E, Karssen LC, Lehtimäki T, Lyssenko V, Magnusson PKE, Mihailov E, Müller-Nurasyid M, Mpindi JP, Pedersen NL, Penninx BWJH, Perola M, Pers TH, Peters A, Rung J, Smit JH, Steinthorsdottir V, Tobin MD, Tsernikova N, van Leeuwen EM, Viikari JS, Willems SM, Willemsen G, Schunkert H, Erdmann J, Samani NJ, Kaprio J, Lind L, Gieger C, Metspalu A, Slagboom PE, Groop L, van Duijn CM, Eriksson JG, Jula A, Salomaa V, Boomsma DI, Power C, Raitakari OT, Ingelsson E, Järvelin MR, Stefansson K, Franke L, Ikonen E, Kallioniemi O, Pietiäinen V, Lindgren CM, Thorsteinsdottir U, Palotie A, McCarthy MI, Morris AP, Prokopenko I, Ripatti S. The impact of low-frequency and rare variants on lipid levels. Nat Genet 2015; 47:589-97. [PMID: 25961943 PMCID: PMC4757735 DOI: 10.1038/ng.3300] [Citation(s) in RCA: 241] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 04/16/2015] [Indexed: 12/18/2022]
Abstract
Using a genome-wide screen of 9.6 million genetic variants achieved through 1000 Genomes Project imputation in 62,166 samples, we identify association to lipid traits in 93 loci, including 79 previously identified loci with new lead SNPs and 10 new loci, 15 loci with a low-frequency lead SNP and 10 loci with a missense lead SNP, and 2 loci with an accumulation of rare variants. In six loci, SNPs with established function in lipid genetics (CELSR2, GCKR, LIPC and APOE) or candidate missense mutations with predicted damaging function (CD300LG and TM6SF2) explained the locus associations. The low-frequency variants increased the proportion of variance explained, particularly for low-density lipoprotein cholesterol and total cholesterol. Altogether, our results highlight the impact of low-frequency variants in complex traits and show that imputation offers a cost-effective alternative to resequencing.
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Affiliation(s)
- Ida Surakka
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
- Public Health Genomics Unit, National Institute for Health and Welfare, Helsinki, Finland
| | - Momoko Horikoshi
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
| | - Reedik Mägi
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Antti-Pekka Sarin
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
- Public Health Genomics Unit, National Institute for Health and Welfare, Helsinki, Finland
| | - Anubha Mahajan
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Vasiliki Lagou
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
| | - Letizia Marullo
- Department of Life Sciences and Biotechnology, Genetic Section, University of Ferrara, Ferrara, Italy
| | - Teresa Ferreira
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Benjamin Miraglio
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
| | - Sanna Timonen
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
| | - Johannes Kettunen
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
| | - Matti Pirinen
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
| | - Juha Karjalainen
- University of Croningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | | | - Sara Hägg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jouke-Jan Hottenga
- Department of Biological Psychology, EMGO institute for Health and Care research, VU University & VU medical center, Amsterdam, The Netherlands
| | - Aaron Isaacs
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
- Centre for Medical Systems Biology, Leiden, the Netherlands
| | - Claes Ladenvall
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University Diabetes Centre, Skåne University Hospital, Malmö, Sweden
| | - Marian Beekman
- Department of Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
- Netherlands Consortium for Healthy Ageing, Leiden, The Netherlands
| | - Tõnu Esko
- Estonian Genome Center, University of Tartu, Tartu, Estonia
- Divisions of Endocrinology and Center for Basic and Translational Obesity Research, Children's Hospital, Boston, Massachusetts, USA
- The Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Janina S Ried
- Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Christopher P Nelson
- Department of Cardiovascular Sciences, University of Leicester, Leicester, LE3 9QP, UK
- National Institute for Health Research (NIHR) Leicester Cardiovascular Disease Biomedical Research Unit, Glenfield Hospital, Leicester, UK
| | - Christina Willenborg
- Institut für Integrative und Experimentelle Genomik, Universität zu Lübeck, Lübeck, Germany
- Deutsches Zentrum für Herz-Kreislauf-Forschung e. V. (DZHK), Partnersite Hamburg, Lübeck, Kiel, Germany
| | - Stefan Gustafsson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Harm-Jan Westra
- University of Croningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Matthew Blades
- Bioinformatics and Biostatistics Support Hub (B/BASH), University of Leicester, University Road, Leicester, UK
| | - Anton JM de Craen
- Department of Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, The Netherlands
| | - Eco J de Geus
- Department of Biological Psychology, EMGO institute for Health and Care research, VU University & VU medical center, Amsterdam, The Netherlands
| | - Joris Deelen
- Department of Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
- Netherlands Consortium for Healthy Ageing, Leiden, The Netherlands
| | - Harald Grallert
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München - Germany Research Center for Environmental Health, Neuherberg, Germany
| | - Anders Hamsten
- Cardiovascular Genetics and Genomics Group, Atherosclerosis Research Unit, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Aki S. Havulinna
- Unit of Chronic Disease Epidemiology and Prevention, National Institute for Health and Welfare, Helsinki, Finland
| | - Christian Hengstenberg
- Deutsches Herzzentrum München, Technische Universität München, München, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany
| | | | - Elina Hyppönen
- Centre for Paediatric Epidemiology and Biostatistics, UCL Institute of Child Health, London, UK
- South Australian Health and Medical Research Institute, Adelaide, Australia
- School of population Health and Sansom Institute, University of South Australia, Adelaide, Australia
| | - Lennart C Karssen
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories and School of Medicine, University of Tampere, Tampere, Finland
| | - Valeriya Lyssenko
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University Diabetes Centre, Skåne University Hospital, Malmö, Sweden
- Steno Diabetes Center A/S, Gentofte, Denmark
| | - Patrik KE Magnusson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | | | - Martina Müller-Nurasyid
- Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany
- Department of Medicine I, University Hospital Grosshadern, Ludwig-Maximilians-Universität, Munich, Germany
- Institute of Medical Informatics, Biometry and Epidemiology, Chair of Genetic Epidemiology, Ludwig-Maximilians-Universität, Munich, Germany
| | - John-Patrick Mpindi
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
| | - Nancy L Pedersen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Brenda WJH Penninx
- Department of Psychiatry, VU University Medical Center, Amsterdam, The Netherlands
| | - Markus Perola
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
- Public Health Genomics Unit, National Institute for Health and Welfare, Helsinki, Finland
| | - Tune H Pers
- Divisions of Endocrinology and Center for Basic and Translational Obesity Research, Children's Hospital, Boston, Massachusetts, USA
- The Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA
- Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
| | - Annette Peters
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München - Germany Research Center for Environmental Health, Neuherberg, Germany
- Deutsches Herzzentrum München, Technische Universität München, München, Germany
| | - Johan Rung
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Johannes H Smit
- Department of Psychiatry, VU University Medical Center, Amsterdam, The Netherlands
| | | | - Martin D Tobin
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, University Road, Leicester, UK
| | | | - Elisabeth M van Leeuwen
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Jorma S Viikari
- Department of Medicine, University of Turku and Division of Medicine, Turku University Hospital, Turku, Finland
| | - Sara M Willems
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Gonneke Willemsen
- Department of Biological Psychology, EMGO institute for Health and Care research, VU University & VU medical center, Amsterdam, The Netherlands
| | - Heribert Schunkert
- Deutsches Herzzentrum München, Technische Universität München, München, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany
| | - Jeanette Erdmann
- Institut für Integrative und Experimentelle Genomik, Universität zu Lübeck, Lübeck, Germany
- Deutsches Zentrum für Herz-Kreislauf-Forschung e. V. (DZHK), Partnersite Hamburg, Lübeck, Kiel, Germany
| | - Nilesh J Samani
- Department of Cardiovascular Sciences, University of Leicester, Leicester, LE3 9QP, UK
- National Institute for Health Research (NIHR) Leicester Cardiovascular Disease Biomedical Research Unit, Glenfield Hospital, Leicester, UK
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
- Hjelt Institute, University of Helsinki, Helsinki, Finland
- Department of Mental Health and Substance Abuse Services, National Institute for Health and Welfare, Helsinki, Finland
| | - Lars Lind
- Department of Medical Sciences, Uppsala University, Akademiska Sjukhuset, Uppsala, Sweden
| | - Christian Gieger
- Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Andres Metspalu
- Estonian Genome Center, University of Tartu, Tartu, Estonia
- The Institute of Molecular and Cell Biology of the University of Tartu, Tartu, Estonia
| | - P Eline Slagboom
- Department of Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
- Netherlands Consortium for Healthy Ageing, Leiden, The Netherlands
| | - Leif Groop
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University Diabetes Centre, Skåne University Hospital, Malmö, Sweden
| | - Cornelia M van Duijn
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
- Centre for Medical Systems Biology, Leiden, the Netherlands
| | - Johan G Eriksson
- Department of General Practice and Primary Health Care, University of Helsinki, Helsinki, Finland
- Folkhälsan Research Centre, Helsinki, Finland
- Helsinki University Hospital, Unit of Primary Health Care, Helsinki, Finland
- Department of Health Promotion and Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland
| | - Antti Jula
- Department of Chronic Disease Prevention, National Institute for Health and Welfare, Turku, Finland
| | - Veikko Salomaa
- Unit of Chronic Disease Epidemiology and Prevention, National Institute for Health and Welfare, Helsinki, Finland
| | - Dorret I Boomsma
- Department of Biological Psychology, EMGO institute for Health and Care research, VU University & VU medical center, Amsterdam, The Netherlands
| | - Christine Power
- Centre for Paediatric Epidemiology and Biostatistics, UCL Institute of Child Health, London, UK
| | - Olli T Raitakari
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Finland
- Department of Clinical Physiology and Nuclear Medicine, University of Turku and Turku University Hospital, Finland
| | - Erik Ingelsson
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Marjo-Riitta Järvelin
- Department of Epidemiology and Biostatistics, MRC Health Protection Agency (HPE), Centre for Environment and Health, School of Public Health, Imperial College London, UK
- Institute of Health Sciences, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Unit of Primary Care, Oulu University Hospital, Oulu, Finland
- Department of Children and Young People and Families, National Institute for Health Welfare, Oulu, Finland
| | - Kari Stefansson
- deCODE Genetics/Amgen inc., Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Lude Franke
- University of Croningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Elina Ikonen
- Institute of Biomedicine, Anatomy, University of Helsinki, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | - Olli Kallioniemi
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
| | - Vilja Pietiäinen
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
| | - Cecilia M Lindgren
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- The Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA
| | - Unnur Thorsteinsdottir
- deCODE Genetics/Amgen inc., Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Aarno Palotie
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
- Public Health Genomics Unit, National Institute for Health and Welfare, Helsinki, Finland
- The Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA
- Haartman Institute, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Mark I McCarthy
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
- Oxford National Institute for Health Research (NIHR) Biomedical Research Centre, Churchill Hospital, Oxford, UK
| | - Andrew P Morris
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Estonian Genome Center, University of Tartu, Tartu, Estonia
- Department of Biostatistics, University of Liverpool, Liverpool, UK
| | - Inga Prokopenko
- Department of Genomics of Common Disease, School of Public Health, Imperial College London, Hammersmith Hospital, London, UK
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
- Hjelt Institute, University of Helsinki, Helsinki, Finland
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
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