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van Leeuwen EM, Sabo A, Bis JC, Huffman JE, Manichaikul A, Smith AV, Feitosa MF, Demissie S, Joshi PK, Duan Q, Marten J, van Klinken JB, Surakka I, Nolte IM, Zhang W, Mbarek H, Li-Gao R, Trompet S, Verweij N, Evangelou E, Lyytikäinen LP, Tayo BO, Deelen J, van der Most PJ, van der Laan SW, Arking DE, Morrison A, Dehghan A, Franco OH, Hofman A, Rivadeneira F, Sijbrands EJ, Uitterlinden AG, Mychaleckyj JC, Campbell A, Hocking LJ, Padmanabhan S, Brody JA, Rice KM, White CC, Harris T, Isaacs A, Campbell H, Lange LA, Rudan I, Kolcic I, Navarro P, Zemunik T, Salomaa V, Kooner AS, Kooner JS, Lehne B, Scott WR, Tan ST, de Geus EJ, Milaneschi Y, Penninx BWJH, Willemsen G, de Mutsert R, Ford I, Gansevoort RT, Segura-Lepe MP, Raitakari OT, Viikari JS, Nikus K, Forrester T, McKenzie CA, de Craen AJM, de Ruijter HM, Pasterkamp G, Snieder H, Oldehinkel AJ, Slagboom PE, Cooper RS, Kähönen M, Lehtimäki T, Elliott P, van der Harst P, Jukema JW, Mook-Kanamori DO, Boomsma DI, Chambers JC, Swertz M, Ripatti S, Willems van Dijk K, Vitart V, Polasek O, Hayward C, Wilson JG, Wilson JF, Gudnason V, Rich SS, Psaty BM, Borecki IB, Boerwinkle E, Rotter JI, Cupples LA, van Duijn CM. Meta-analysis of 49 549 individuals imputed with the 1000 Genomes Project reveals an exonic damaging variant in ANGPTL4 determining fasting TG levels. J Med Genet 2016; 53:441-9. [PMID: 27036123 PMCID: PMC4941146 DOI: 10.1136/jmedgenet-2015-103439] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 11/23/2015] [Indexed: 01/22/2023]
Abstract
Background So far, more than 170 loci have been associated with circulating lipid levels through genome-wide association studies (GWAS). These associations are largely driven by common variants, their function is often not known, and many are likely to be markers for the causal variants. In this study we aimed to identify more new rare and low-frequency functional variants associated with circulating lipid levels. Methods We used the 1000 Genomes Project as a reference panel for the imputations of GWAS data from ∼60 000 individuals in the discovery stage and ∼90 000 samples in the replication stage. Results Our study resulted in the identification of five new associations with circulating lipid levels at four loci. All four loci are within genes that can be linked biologically to lipid metabolism. One of the variants, rs116843064, is a damaging missense variant within the ANGPTL4 gene. Conclusions This study illustrates that GWAS with high-scale imputation may still help us unravel the biological mechanism behind circulating lipid levels.
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Affiliation(s)
| | - Aniko Sabo
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, USA
| | - Joshua C Bis
- Department of Medicine, University of Washington, Seattle, USA
| | - Jennifer E Huffman
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK The Framingham Heart Study, NHLBI Cardiovascular Epidemiology and Human Genomics Branch, Framingham, USA
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, USA
| | - Albert V Smith
- Icelandic Heart Association, Kopavogur, Iceland Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Mary F Feitosa
- Department of Genetics, Washington University School of Medicine, St Louis, USA
| | - Serkalem Demissie
- Department of Biostatistics, Boston University School of Public Health, Boston, USA
| | - Peter K Joshi
- Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Qing Duan
- Department of Genetics, University of North Carolina, Chapel Hill, USA
| | - Jonathan Marten
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Jan B van Klinken
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Ida Surakka
- Human Genomics Unit, Institute for Molecular Medicine, University of Helsinki, Helsinki, Finland
| | - Ilja M Nolte
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Weihua Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK Department of Cardiology, Ealing Hospital NHS Trust, Middlesex, UK
| | - Hamdi Mbarek
- Department of Biological Psychology, VU University Amsterdam and EMGO+ Institute for Health and Care Research, Amsterdam, The Netherlands
| | - Ruifang Li-Gao
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Stella Trompet
- Department of Cardiology, Leiden University Medical Center, Leiden, The Netherlands Department of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, The Netherlands
| | - Niek Verweij
- Department of Cardiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Evangelos Evangelou
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK Department of Hygiene and Epidemiology, University of Ioannina Medical School, Ioannina, Greece
| | - Leo-Pekka Lyytikäinen
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland Department of Clinical Chemistry, University of Tampere School of Medicine, Tampere, Finland
| | - Bamidele O Tayo
- Public Health Sciences, Loyola University Chicago Stritch School of Medicine, Maywood, USA
| | - Joris Deelen
- Department of Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter J van der Most
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Sander W van der Laan
- Laboratory of Experimental Cardiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Dan E Arking
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Alanna Morrison
- Human Genetics Center, The University of Texas School of Public Health, Houston, USA
| | - Abbas Dehghan
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Oscar H Franco
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Albert Hofman
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Fernando Rivadeneira
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Eric J Sijbrands
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Andre G Uitterlinden
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Josyf C Mychaleckyj
- Center for Public Health Genomics, University of Virginia, Charlottesville, USA
| | - Archie Campbell
- Generation Scotland, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Lynne J Hocking
- Musculoskeletal Research Programme, Division of Applied Medicine, University of Aberdeen, Aberdeen, UK
| | - Sandosh Padmanabhan
- British Heart Foundation Glasgow Cardiovascular Research Centre, Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | | | - Kenneth M Rice
- Department of Biostatistics, University of Washington, Seattle, USA
| | | | - Tamara Harris
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Bethesda, USA
| | - Aaron Isaacs
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Harry Campbell
- Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Leslie A Lange
- Department of Genetics, University of North Carolina, Chapel Hill, USA
| | - Igor Rudan
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, UK
| | - Ivana Kolcic
- Faculty of Medicine, University of Split, Split, Croatia
| | - Pau Navarro
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | | | - Veikko Salomaa
- Department of Health, National Institute for Health and Welfare, Helsinki, Finland
| | | | - Angad S Kooner
- Cardiovascular Science, National Heart and Lung Institute, Imperial College London, London, UK
| | - Jaspal S Kooner
- Department of Cardiology, Ealing Hospital NHS Trust, Middlesex, UK Cardiovascular Science, National Heart and Lung Institute, Imperial College London, London, UK Imperial College Healthcare NHS Trus, Imperial College London, London, UK
| | - Benjamin Lehne
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - William R Scott
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK Department of Cardiology, Ealing Hospital NHS Trust, Middlesex, UK
| | - Sian-Tsung Tan
- Cardiovascular Science, National Heart and Lung Institute, Imperial College London, London, UK
| | - Eco J de Geus
- Department of Biological Psychology, VU University Amsterdam and EMGO+ Institute for Health and Care Research, Amsterdam, The Netherlands
| | - Yuri Milaneschi
- Department of Psychiatry, VU University Medical Center Amsterdam/GGZinGeest and EMGO+ Institute for Health and Care Research and Neuroscience Campus Amsterdam, Amsterdam, The Netherlands
| | - Brenda W J H Penninx
- Department of Psychiatry, VU University Medical Center Amsterdam/GGZinGeest and EMGO+ Institute for Health and Care Research and Neuroscience Campus Amsterdam, Amsterdam, The Netherlands
| | - Gonneke Willemsen
- Department of Biological Psychology, VU University Amsterdam and EMGO+ Institute for Health and Care Research, Amsterdam, The Netherlands
| | - Renée de Mutsert
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Ian Ford
- Robertson Center for Biostatistics, University of Glasgow, Glasgow, UK
| | - Ron T Gansevoort
- Department of Nephrology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Marcelo P Segura-Lepe
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Olli T Raitakari
- Department of Clinical Physiology, Turku University Hospital, Turku, Finland Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
| | - Jorma S Viikari
- Division of Medicine, Turku University Hospital, Turku, Finland Department of Medicine, University of Turku, Turku, Finland
| | - Kjell Nikus
- Department of Cardiology, Heart Hospital, Tampere University Hospital, Tampere, Finland School of Medicine, University of Tampere, Tampere, Finland
| | - Terrence Forrester
- Tropical Metabolism Research Unit, Tropical Medicine Research Institute, University of the West Indies, Mona, Jamaica
| | - Colin A McKenzie
- Tropical Metabolism Research Unit, Tropical Medicine Research Institute, University of the West Indies, Mona, Jamaica
| | - Anton J M de Craen
- Department of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, The Netherlands
| | - Hester M de Ruijter
- Laboratory of Experimental Cardiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Gerard Pasterkamp
- Laboratory of Experimental Cardiology, University Medical Center Utrecht, Utrecht, The Netherlands Laboratory of Clinical Chemistry and Hematology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Albertine J Oldehinkel
- Department of Psychiatry, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - P Eline Slagboom
- Department of Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Richard S Cooper
- Public Health Sciences, Loyola University Chicago Stritch School of Medicine, Maywood, USA
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital, Tampere, Finland Department of Clinical Physiology, University of Tampere School of Medicine, Tampere, Finland
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland Department of Clinical Chemistry, University of Tampere School of Medicine, Tampere, Finland
| | - Paul Elliott
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
| | - Pim van der Harst
- Department of Cardiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - J Wouter Jukema
- Department of Cardiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Dennis O Mook-Kanamori
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, The Netherlands Department of Public Health and Primary Care, Leiden University Medical Center, Leiden, The Netherlands Epidemiology Section, Department of BESC, King Faisal Medical Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Dorret I Boomsma
- Department of Biological Psychology, VU University Amsterdam and EMGO+ Institute for Health and Care Research, Amsterdam, The Netherlands
| | - John C Chambers
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK Department of Cardiology, Ealing Hospital NHS Trust, Middlesex, UK Imperial College Healthcare NHS Trus, Imperial College London, London, UK
| | - Morris Swertz
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands Genomics Coordination Center, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Samuli Ripatti
- Human Genomics Unit, Institute for Molecular Medicine, University of Helsinki, Helsinki, Finland Public Health, University of Helsinki, Helsinki, Finland Wellcome Trust Sanger Institute, UK
| | - Ko Willems van Dijk
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands Department of General Internal Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Veronique Vitart
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Ozren Polasek
- Faculty of Medicine, University of Split, Split, Croatia
| | - Caroline Hayward
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - James G Wilson
- Physiology and Biophysics, University of Mississippi Medical Center, Jackson, USA
| | - James F Wilson
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Vilmundur Gudnason
- Icelandic Heart Association, Kopavogur, Iceland Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, USA
| | - Bruce M Psaty
- Department of Medicine, University of Washington, Seattle, USA Department of Epidemiology, University of Washington, Seattle, USA Department of Health Services, University of Washington, Seattle, USA Group Health Cooperative, Group Health Research Institute, Seattle, USA
| | - Ingrid B Borecki
- Department of Genetics, Washington University School of Medicine, St Louis, USA
| | - Eric Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, USA Human Genetics Center, The University of Texas School of Public Health, Houston, USA
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences, Los Angeles BioMedical Research Institute at Harbor-UCLA Medical Center, Torrance, USA Division of Genomic Outcomes, Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, USA Departments of Pediatrics, Medicine, and Human Genetics, UCLA, Los Angeles, USA
| | - L Adrienne Cupples
- The Framingham Heart Study, NHLBI Cardiovascular Epidemiology and Human Genomics Branch, Framingham, USA Department of Genetics, Washington University School of Medicine, St Louis, USA
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