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van Leeuwen EM, Huffman JE, Bis JC, Isaacs A, Mulder M, Sabo A, Smith AV, Demissie S, Manichaikul A, Brody JA, Feitosa MF, Duan Q, Schraut KE, Navarro P, van Vliet-Ostaptchouk JV, Zhu G, Mbarek H, Trompet S, Verweij N, Lyytikäinen LP, Deelen J, Nolte IM, van der Laan SW, Davies G, Vermeij-Verdoold AJ, van Oosterhout AA, Vergeer-Drop JM, Arking DE, Trochet H, Medina-Gomez C, Rivadeneira F, Uitterlinden AG, Dehghan A, Franco OH, Sijbrands EJ, Hofman A, White CC, Mychaleckyj JC, Peloso GM, Swertz MA, Willemsen G, de Geus EJ, Milaneschi Y, Penninx BW, Ford I, Buckley BM, de Craen AJ, Starr JM, Deary IJ, Pasterkamp G, Oldehinkel AJ, Snieder H, Slagboom PE, Nikus K, Kähönen M, Lehtimäki T, Viikari JS, Raitakari OT, van der Harst P, Jukema JW, Hottenga JJ, Boomsma DI, Whitfield JB, Montgomery G, Martin NG, Polasek O, Vitart V, Hayward C, Kolcic I, Wright AF, Rudan I, Joshi PK, Wilson JF, Lange LA, Wilson JG, Gudnason V, Harris TB, Morrison AC, Borecki IB, Rich SS, Padmanabhan S, Psaty BM, Rotter JI, Smith BH, Boerwinkle E, Cupples LA, van Duijn C. Fine mapping the CETP region reveals a common intronic insertion associated to HDL-C. NPJ Aging Mech Dis 2015; 1:15011. [PMID: 28721259 PMCID: PMC5514988 DOI: 10.1038/npjamd.2015.11] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Revised: 07/24/2015] [Accepted: 08/10/2015] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Individuals with exceptional longevity and their offspring have significantly larger high-density lipoprotein concentrations (HDL-C) particle sizes due to the increased homozygosity for the I405V variant in the cholesteryl ester transfer protein (CETP) gene. In this study, we investigate the association of CETP and HDL-C further to identify novel, independent CETP variants associated with HDL-C in humans. METHODS We performed a meta-analysis of HDL-C within the CETP region using 59,432 individuals imputed with 1000 Genomes data. We performed replication in an independent sample of 47,866 individuals and validation was done by Sanger sequencing. RESULTS The meta-analysis of HDL-C within the CETP region identified five independent variants, including an exonic variant and a common intronic insertion. We replicated these 5 variants significantly in an independent sample of 47,866 individuals. Sanger sequencing of the insertion within a single family confirmed segregation of this variant. The strongest reported association between HDL-C and CETP variants, was rs3764261; however, after conditioning on the five novel variants we identified the support for rs3764261 was highly reduced (βunadjusted=3.179 mg/dl (P value=5.25×10-509), βadjusted=0.859 mg/dl (P value=9.51×10-25)), and this finding suggests that these five novel variants may partly explain the association of CETP with HDL-C. Indeed, three of the five novel variants (rs34065661, rs5817082, rs7499892) are independent of rs3764261. CONCLUSIONS The causal variants in CETP that account for the association with HDL-C remain unknown. We used studies imputed to the 1000 Genomes reference panel for fine mapping of the CETP region. We identified and validated five variants within this region that may partly account for the association of the known variant (rs3764261), as well as other sources of genetic contribution to HDL-C.
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Affiliation(s)
| | - Jennifer E Huffman
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Edinburgh, UK.,National Heart, Lung, and Blood Institute (NHLBI) Cardiovascular Epidemiology and Human Genomics Branch, Framingham Heart Study, Framingham, MA, USA
| | - Joshua C Bis
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Aaron Isaacs
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Monique Mulder
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Aniko Sabo
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Albert V Smith
- Icelandic Heart Association, Kopavogur, Iceland.,Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Serkalem Demissie
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Ani Manichaikul
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Jennifer A Brody
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Mary F Feitosa
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
| | - Qing Duan
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Katharina E Schraut
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, Scotland
| | - Pau Navarro
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Edinburgh, UK
| | - Jana V van Vliet-Ostaptchouk
- Department of Endocrinology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Gu Zhu
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Hamdi Mbarek
- Department of Biological Psychology, VU University Amsterdam and EMGO Institute for Health and Care Research, Amsterdam, 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 of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Leo-Pekka Lyytikäinen
- Department of Clinical Chemistry, Fimlab Laboratories and University of Tampere School of Medicine, Tampere, Finland
| | - Joris Deelen
- Department of Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Ilja M Nolte
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Gail Davies
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK.,Department of Psychology, University of Edinburgh, Edinburgh, UK
| | | | | | | | - Dan E Arking
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Holly Trochet
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Edinburgh, UK
| | | | - Carolina Medina-Gomez
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands.,Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Fernando Rivadeneira
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands.,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
| | - Abbas Dehghan
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Oscar H Franco
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Eric J Sijbrands
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Albert Hofman
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Charles C White
- Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Departments of Neurology and Psychiatry, Brigham and Women's Hospital, Boston, MA, USA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA.,Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, USA
| | - Josyf C Mychaleckyj
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Gina M Peloso
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, USA.,Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA.,Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Morris A Swertz
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Gonneke Willemsen
- Department of Biological Psychology, VU University Amsterdam and EMGO Institute for Health and Care Research, Amsterdam, The Netherlands
| | - 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 Wjh 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
| | - Ian Ford
- Robertson Center for Biostatistics, University of Glasgow, Glasgow, UK
| | - Brendan M Buckley
- Department of Pharmacology and Therapeutics, University College Cork, Cork, Ireland.,Alzheimer Scotland Dementia Research Centre, University of Edinburgh, Edinburgh, UK
| | - Anton Jm de Craen
- Department of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, The Netherlands
| | - John M Starr
- Department of Pharmacology and Therapeutics, University College Cork, Cork, Ireland.,Alzheimer Scotland Dementia Research Centre, University of Edinburgh, Edinburgh, UK
| | - Ian J Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK.,Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Gerard Pasterkamp
- Laboratory of Clinical Chemistry and Hematology, Division Laboratories & Pharmacy, UMC Utrecht, Utrecht, the Netherlands
| | - Albertine J Oldehinkel
- Interdisciplinary Center Psychopathology and Emotion Regulation, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - P Eline Slagboom
- Department of Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Kjell Nikus
- Department of Cardiology, Heart Centre, Tampere University Hospital and University of Tampere School of Medicine, Tampere, Finland
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital and University of Tampere School of Medicine, Tampere, Finland
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories and University of Tampere School of Medicine, Tampere, Finland
| | - Jorma S Viikari
- Division of Medicine, Turku University Hospital, and Department of Medicine, University of Turku, Turku, Finland
| | - Olli T Raitakari
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, and Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland.,Molecular Epidemiology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Pim van der Harst
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - J Wouter Jukema
- Department of Cardiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Jouke-Jan Hottenga
- Department of Biological Psychology, VU University Amsterdam and EMGO Institute for Health and Care Research, Amsterdam, The Netherlands
| | - Dorret I Boomsma
- Department of Biological Psychology, VU University Amsterdam and EMGO Institute for Health and Care Research, Amsterdam, The Netherlands
| | - John B Whitfield
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Grant Montgomery
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, and Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland.,Molecular Epidemiology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Nicholas G Martin
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | | | - Ozren Polasek
- Department of Public Health, Faculty of Medicine, University of Split, Split, Croatia
| | - Veronique Vitart
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Edinburgh, UK
| | - Caroline Hayward
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Edinburgh, UK
| | - Ivana Kolcic
- Department of Public Health, Faculty of Medicine, University of Split, Split, Croatia
| | - Alan F Wright
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Edinburgh, UK
| | - Igor Rudan
- Centre for Population Health Sciences, Medical School, University of Edinburgh, Edinburgh, UK
| | - Peter K Joshi
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, Scotland
| | - James F Wilson
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, Scotland
| | - Leslie A Lange
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - James G Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS, USA
| | - Vilmundur Gudnason
- Icelandic Heart Association, Kopavogur, Iceland.,Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Tamar B Harris
- National Institute on Aging, National Institute of Health, Bethesda, MD, USA
| | - Alanna C Morrison
- Human Genetics Center, The University of Texas School of Public Health, Houston, TX, USA
| | - Ingrid B Borecki
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
| | - Stephen S Rich
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Sandosh Padmanabhan
- Division of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - Bruce M Psaty
- Department of Medicine, Epidemiology & Health Services, University of Washington, Seattle, WA, USA.,Group Health Research Institute, Group Health cooperative, Seattle, WA, USA
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences, Los Angeles BioMedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA.,Division of Genomic Outcomes, Departments of Pediatrics and Medicine, Harbor-UCLA Medical Center, Torrance, CA, USA.,Departments of Pediatrics, Medicine, and Human Genetics, UCLA, Los Angeles, CA, USA
| | - Blair H Smith
- Medical Research Institute, University of Dundee, Dundee, UK
| | - Eric Boerwinkle
- Human Genetics Center, The University of Texas School of Public Health, Houston, TX, USA
| | - L Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA.,Framingham Heart Study, Framingham, MA, USA
| | - Cornelia van Duijn
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
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