Abstract

Vitamin D is a steroid hormone precursor that is associated with a range of human traits and diseases. Previous GWAS of serum 25-hydroxyvitamin D concentrations have identified four genome-wide significant loci (GC, NADSYN1/DHCR7, CYP2R1, CYP24A1). In this study, we expand the previous SUNLIGHT Consortium GWAS discovery sample size from 16,125 to 79,366 (all European descent). This larger GWAS yields two additional loci harboring genome-wide significant variants (P = 4.7×10−9 at rs8018720 in SEC23A, and P = 1.9×10−14 at rs10745742 in AMDHD1). The overall estimate of heritability of 25-hydroxyvitamin D serum concentrations attributable to GWAS common SNPs is 7.5%, with statistically significant loci explaining 38% of this total. Further investigation identifies signal enrichment in immune and hematopoietic tissues, and clustering with autoimmune diseases in cell-type-specific analysis. Larger studies are required to identify additional common SNPs, and to explore the role of rare or structural variants and gene–gene interactions in the heritability of circulating 25-hydroxyvitamin D levels.

Details

Title
Genome-wide association study in 79,366 European-ancestry individuals informs the genetic architecture of 25-hydroxyvitamin D levels
Author
Jiang, Xia 1 ; Paul F O’Reilly 2 ; Aschard, Hugues 3   VIAFID ORCID Logo  ; Yi-Hsiang Hsu 4 ; Richards, J Brent 5   VIAFID ORCID Logo  ; Dupuis, Josée 6 ; Ingelsson, Erik 7 ; Karasik, David 8 ; Pilz, Stefan 9 ; Berry, Diane 10 ; Kestenbaum, Bryan 11 ; Zheng, Jusheng 12 ; Luan, Jianan 12 ; Sofianopoulou, Eleni 13 ; Streeten, Elizabeth A 14 ; Albanes, Demetrius 15 ; Lutsey, Pamela L 16 ; Lu, Yao 16 ; Tang, Weihong 16 ; Econs, Michael J 17 ; Wallaschofski, Henri 18 ; Völzke, Henry 19 ; Zhou, Ang 20 ; Power, Chris 10 ; McCarthy, Mark I 21   VIAFID ORCID Logo  ; Michos, Erin D 22 ; Boerwinkle, Eric 23 ; Weinstein, Stephanie J 15 ; Freedman, Neal D 15 ; Wen-Yi, Huang 24 ; Van Schoor, Natasja M 25 ; van der Velde, Nathalie 26 ; Lisette C P G M de Groot 27   VIAFID ORCID Logo  ; Enneman, Anke 28 ; Cupples, L Adrienne 6 ; Booth, Sarah L 29 ; Vasan, Ramachandran S 30 ; Liu, Ching-Ti 31   VIAFID ORCID Logo  ; Zhou, Yanhua 31 ; Ripatti, Samuli 32 ; Ohlsson, Claes 33 ; Vandenput, Liesbeth 33 ; Lorentzon, Mattias 34 ; Eriksson, Johan G 35 ; Shea, M Kyla 29 ; Houston, Denise K 36 ; Kritchevsky, Stephen B 36 ; Liu, Yongmei 37 ; Lohman, Kurt K 38 ; Ferrucci, Luigi 39 ; Peacock, Munro 17 ; Gieger, Christian 40 ; Beekman, Marian 41   VIAFID ORCID Logo  ; Slagboom, Eline 41 ; Deelen, Joris 42   VIAFID ORCID Logo  ; Diana van Heemst 43 ; Kleber, Marcus E 44   VIAFID ORCID Logo  ; März, Winfried 45 ; de Boer, Ian H 46 ; Wood, Alexis C 47 ; Rotter, Jerome I 48 ; Rich, Stephen S 49 ; Robinson-Cohen, Cassianne 50 ; Martin den Heijer 51 ; Jarvelin, Marjo-Riitta 52 ; Cavadino, Alana 53 ; Joshi, Peter K 54   VIAFID ORCID Logo  ; Wilson, James F 55   VIAFID ORCID Logo  ; Hayward, Caroline 56   VIAFID ORCID Logo  ; Lind, Lars 57 ; Michaëlsson, Karl 58 ; Trompet, Stella 59 ; Zillikens, M Carola 51 ; Uitterlinden, Andre G 60 ; Rivadeneira, Fernando 60   VIAFID ORCID Logo  ; Broer, Linda 51 ; Zgaga, Lina 61 ; Campbell, Harry 62 ; Theodoratou, Evropi 62 ; Farrington, Susan M 63   VIAFID ORCID Logo  ; Timofeeva, Maria 63 ; Dunlop, Malcolm G 63 ; Valdes, Ana M 64 ; Tikkanen, Emmi 65 ; Lehtimäki, Terho 66 ; Leo-Pekka Lyytikäinen 66   VIAFID ORCID Logo  ; Kähönen, Mika 67 ; Raitakari, Olli T 68 ; Mikkilä, Vera 69 ; Ikram, M Arfan 28   VIAFID ORCID Logo  ; Sattar, Naveed 70 ; Jukema, J Wouter 71   VIAFID ORCID Logo  ; Wareham, Nicholas J 12 ; Langenberg, Claudia 12 ; Forouhi, Nita G 12 ; Gundersen, Thomas E 72 ; Kay-Tee Khaw 13 ; Butterworth, Adam S 13 ; Danesh, John 73 ; Spector, Timothy 74 ; Wang, Thomas J 75 ; Hyppönen, Elina 76 ; Kraft, Peter 77 ; Kiel, Douglas P 4 

 Program in Genetic Epidemiology and Statistical Genetics. Department of Epidemiology, Harvard T.H.Chan School of Public Health, Boston, MA, USA; Unit of Cardiovascular Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden 
 Department of Social Genetic & Developmental Psychiatry, King’s College London, Institute of Psychiatry, London, UK 
 Program in Genetic Epidemiology and Statistical Genetics. Department of Epidemiology, Harvard T.H.Chan School of Public Health, Boston, MA, USA; Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI), Institut Pasteur, Paris, France 
 Institute for Aging Research, Boston, MA, USA; Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA; Broad Institute of Harvard and Massachusetts Institute of Technology, Boston, MA, USA 
 Departments of Medicine, Human Genetics, Epidemiology and Biostatistics, Québec, Canada 
 Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA; Framingham Heart Study, Framingham, MA, USA 
 Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine Stanford, Stanford, CA, USA; Department of Medical Sciences, Uppsala University, Uppsala, Sweden 
 Institute for Aging Research, Boston, MA, USA 
 Department of Internal Medicine, Division of Endocrinology and Diabetology, Medical University of Graz, Graz, Austria 
10  Population, Policy and Practice, University College London, Great Ormond Street, Institute of Child Health, London, UK 
11  Kidney Research Institute, Division of Nephrology, Seattle, WA, USA 
12  MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK 
13  Department of Public Health & Primary Care, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK 
14  Genetics and Personalized Medicine Program, University of Maryland School of Medicine, Baltimore, MD, USA 
15  Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA 
16  Division of Epidemiology & Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, USA 
17  Department of Medicine, Indiana University, Endocrinology, Indianapolis, IN, USA 
18  Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site, Greifswald, Berlin, Germany 
19  DZHK (German Centre for Cardiovascular Research), Partner Site, Greifswald, Berlin, Germany; Institut für Community Medicine, SHIP/Klinisch-Epidemiologische Forschung, Universitätsmedizin Greifswald, Greifswald, Germany 
20  Centre for Population Health Research, Sansom Institute for Health Research, University of South Australia, Adelaide, SA, Australia 
21  Oxford Centre for Diabetes Endocrinology and Metabolism, University of Oxford, Oxford, UK; Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK; Oxford NIHR Biomedical Research Centre, Churchill Hospital, Oxford, UK 
22  Division of Cardiology, Ciccarone Center for the Prevention of Heart Disease, Johns Hopkins School of Medicine, Baltimore, MD, USA; Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA 
23  Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX, USA 
24  Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA 
25  Department of Epidemiology and Biostatistics, Amsterdam Public Health Research Institute, VU University Medical Center, Amsterdam, The Netherlands 
26  Erasmus MC Department of Epidemiology, Rotterdam, The Netherlands; AMC, Internal Medicine, Geriatrics Department, Amsterdam, The Netherlands 
27  Department of Human Nutrition, Wageningen University, Wageningen, The Netherlands 
28  Erasmus MC Department of Epidemiology, Rotterdam, The Netherlands 
29  Vitamin K Laboratory, Jean Mayer USDA Human Nutrition Research Center on Aging, Tufts University, Boston, MA, USA 
30  Framingham Heart Study, Framingham, MA, USA 
31  Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA 
32  Statistical and Translational Genetics, University of Helsinki, Helsinki 2U, Finland 
33  Department of Internal Medicine and Clinical Nutrition, University of Gothenburg, Gothenburg, Sweden 
34  Department of Geriatric Medicine, University of Gothenburg and Sahlgrenska University Hospital, Mölndal, Sweden 
35  Department of General Practice and Primary Health Care, University of Helsinki and Helsinki University Hospital, University of Helsinki, Tukholmankatu, Finland; Folkhälsan Research Center, University of Helsinki, Helsinki, Finland 
36  Sticht Center for Healthy Aging and Alzheimer’s Prevention, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC, USA 
37  Department of Epidemiology and Prevention, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA 
38  Department of Biostatistical Sciences, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA 
39  Longitudinal Studies Section, Intramural Research Program of the National Institute on Aging, NIH, Baltimore, MD, USA 
40  German Research Center for Environmental Health, Molecular Epidemiology, AME, Ingolstädter Landstr 1, Neuherberg, Germany 
41  Molecular Epidemiology, Leiden University Medical Center, Einthovenweg 20, Leiden, The Netherlands 
42  Molecular Epidemiology, Leiden University Medical Center, Einthovenweg 20, Leiden, The Netherlands; Max Planck Institute for Biology of Ageing, Köln (Cologne), Germany 
43  Gerontology and Geriatrics, Leiden University Medical Center, Leiden, The Netherlands 
44  Vth Department of Medicine (Nephrology, Hypertensiology, Rheumatology, Endocrinology, Diabetology), Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany 
45  Vth Department of Medicine (Nephrology, Hypertensiology, Rheumatology, Endocrinology, Diabetology), Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany; Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, Graz, Graz, Austria; SYNLAB Holding Deutschland GmbH, Augsburg, Germany 
46  Division of Nephrology and Kidney Research Institute, University of Washington, Washington, DC, USA 
47  USDA/ARS Children’s Nutrition Research Center, Houston, TX, USA 
48  Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA, USA 
49  Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA; Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA 
50  Division of Nephrology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA 
51  Erasmus MC Department of Internal Medicine, Rotterdam, The Netherlands 
52  Epidemiology and Biostatistics School of Public Health, Imperial College London, London, UK; Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland; Biocenter Oulu, University of Oulu, Aapistie 5A, Finland; Unit of Primary Care, Oulu University Hospital, Kajaanintie 50, Finland 
53  Population, Policy and Practice, University College London, Great Ormond Street, Institute of Child Health, London, UK; Centre for Environmental and Preventive Medicine, Wolfson Institute of Preventive Medicine, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK 
54  Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK 
55  Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK; MRC Human Genetics Unit, MRC Institute of Genetics & Molecular Medicine, the University of Edinburgh, Western General Hospital, Edinburgh, UK 
56  MRC Human Genetics Unit, MRC Institute of Genetics & Molecular Medicine, the University of Edinburgh, Western General Hospital, Edinburgh, UK 
57  Department of Medical Sciences, Uppsala University, Uppsala, Sweden 
58  Department of Surgical Sciences, Uppsala University, Uppsala, Sweden 
59  Gerontology and Geriatrics, Leiden University Medical Center, Leiden, The Netherlands; Department of Cardiology, Leiden University Medical Center, Leiden, Netherlands 
60  Erasmus MC Department of Epidemiology, Rotterdam, The Netherlands; Erasmus MC Department of Internal Medicine, Rotterdam, The Netherlands 
61  Department of Public Health and Primary Care, Institute of Population Health, Trinity College Dublin, University of Dublin, Dublin 24, Ireland 
62  Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK; Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK 
63  Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK 
64  The Department of Twin Research & Genetic Epidemiology, King’s College London, St Thomas’ Campus, London, UK; School of Medicine, University of Nottingham, Nottingham, UK 
65  FIMM-Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland 
66  Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland; Department of Clinical Chemistry, Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland 
67  Department of Clinical Physiology, Tampere University Hospital, Tampere, Finland; Department of Clinical Physiology, Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland 
68  Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland; Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland 
69  Science Adviser at Academy of Finland, Helsinki, Finland 
70  BHF Glasgow Cardiovascular Research Centre, Faculty of Medicine, University Avenue, Glasgow, UK 
71  Department of Cardiology, Leiden University Medical Center, Leiden, Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, The Netherlands 
72  Vitas AS, Oslo, Norway 
73  Department of Public Health & Primary Care, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK; Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK 
74  The Department of Twin Research & Genetic Epidemiology, King’s College London, St Thomas’ Campus, London, UK 
75  Division of Cardiovascular Medicine, Vanderbilt Heart and Vascular Institute, Nashville, TN, USA 
76  Population, Policy and Practice, University College London, Great Ormond Street, Institute of Child Health, London, UK; Centre for Population Health Research, Sansom Institute for Health Research, University of South Australia, Adelaide, SA, Australia 
77  Program in Genetic Epidemiology and Statistical Genetics. Department of Epidemiology, Harvard T.H.Chan School of Public Health, Boston, MA, USA 
Pages
1-12
Publication year
2018
Publication date
Jan 2018
Publisher
Nature Publishing Group
e-ISSN
20411723
Source type
Scholarly Journal
Language of publication
English
ProQuest document ID
1988509826
Copyright
© 2018. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.