Abstract
Homozygosity has long been associated with rare, often devastating, Mendelian disorders1, and Darwin was one of the first to recognize that inbreeding reduces evolutionary fitness2. However, the effect of the more distant parental relatedness that is common in modern human populations is less well understood. Genomic data now allow us to investigate the effects of homozygosity on traits of public health importance by observing contiguous homozygous segments (runs of homozygosity), which are inferred to be homozygous along their complete length. Given the low levels of genome-wide homozygosity prevalent in most human populations, information is required on very large numbers of people to provide sufficient power3,4. Here we use runs of homozygosity to study 16 health-related quantitative traits in 354,224 individuals from 102 cohorts, and find statistically significant associations between summed runs of homozygosity and four complex traits: height, forced expiratory lung volume in one second, general cognitive ability and educational attainment (P < 1 × 10−300, 2.1 × 10−6, 2.5 × 10−10 and 1.8 × 10−10, respectively). In each case, increased homozygosity was associated with decreased trait value, equivalent to the offspring of first cousins being 1.2 cm shorter and having 10 months’ less education. Similar effect sizes were found across four continental groups and populations with different degrees of genome-wide homozygosity, providing evidence that homozygosity, rather than confounding, directly contributes to phenotypic variance. Contrary to earlier reports in substantially smaller samples5,6, no evidence was seen of an influence of genome-wide homozygosity on blood pressure and low density lipoprotein cholesterol, or ten other cardio-metabolic traits. Since directional dominance is predicted for traits under directional evolutionary selection7, this study provides evidence that increased stature and cognitive function have been positively selected in human evolution, whereas many important risk factors for late-onset complex diseases may not have been.
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Acknowledgements
This paper is the work of the ROHgen consortium. We thank the participants in all ROHgen studies; cohort-specific acknowledgements are detailed in Supplementary Table 6. This work was funded by a UK Medical Research Council (MRC) PhD studentship to P.K.J.; and J.F.W. and O.P. acknowledge support from the MRC Human Genetics Unit “QTL in Health and Disease” programme. We thank W. G. Hill for discussions and comments on the manuscript and K. Lindsay for administrative assistance.
Author information
Peter K. Joshi, Tonu Esko, Ozren Polašek and James F. Wilson: These authors contributed equally to this work.
Authors and Affiliations
Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, UK
Peter K. Joshi, Igor Rudan, Harry Campbell, Ozren Polašek & James F. Wilson
Estonian Genome Center, University of Tartu, Riia 23b, 51010, Tartu, Estonia
Tonu Esko, Reedik Mägi, Evelin Mihailov, Lili Milani, Mari Nelis, Natalia Tšernikova, Andrew P. Morris, Andres Metspalu & Markus Perola
Division of Endocrinology and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Cambridge, 02141, Massachusetts, USA
Tonu Esko, Yingleong Chan, Sailaja Vedantam, Rany M. Salem & Joel N. Hirschhorn
Program in Medical and Population Genetics, Broad Institute, Cambridge Center 7, Cambridge, 02242, Massachusetts, USA
Tonu Esko, Yingleong Chan, Sailaja Vedantam, Rany M. Salem, Cecilia M. Lindgren & Joel N. Hirschhorn
Department of Genetics, Harvard Medical School, 25 Shattuck St, Boston, 02115, Massachusetts, USA
Tonu Esko, Yingleong Chan, Sailaja Vedantam, Rany M. Salem & Joel N. Hirschhorn
Unit of Public Health Genomics, National Institute for Health and Welfare, P.O. Box 104, Helsinki, FI-00251, Finland
Hannele Mattsson, Niina Eklund, Anni Joensuu, Antti-Pekka Sarin & Markus Perola
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Hannele Mattsson, Anni Joensuu, Kirsi Pietilainen, Antti-Pekka Sarin & Jaakko Kaprio
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Teresa Nutile, Daniela Ruggiero & Marina Ciullo
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McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, 21205, Maryland, USA
Aravinda Chakravarti & Georg Ehret
Program in Genetic Epidemiology and Statistical Genetics, Harvard School of Public Health, 665 Huntington Ave, Boston, 02115, Massachusetts, USA
Constance Chen & Peter Kraft
Genome Technology Branch, National Human Genome Research Institute, NIH, Bethesda, 20892, Maryland, USA
Francis S. Collins
College of Medicine, Dentistry and Nursing, Ninewells Hospital and Medical School, College Office, Level 10, Dundee, DD1 9SY, UK
John Connell
National Heart, Lung, and Blood Institute's Framingham Heart Study, 73 Mt. Wayte Ave, Framingham, 01702, Massachusetts, USA
L. Adrienne Cupples, Caroline S. Fox, Nancy L. Heard-Costa, George T. O'Connor, Sudha Seshadri & Josée Dupuis
Psychology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
Gail Davies, Paul Redmond & Ian J. Deary
Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
Gail Davies, Sarah E. Harris, David C.M. Liewald, John M. Starr, Ian J. Deary & David J. Porteous
Department of Internal Medicine B, University Medicine Greifswald, Ferdinand-Sauerbruch-Str. NK, Greifswald, 17475, Germany
Marcus Dörr
Cardiology, Geneva University Hospitals, Rue Gabrielle-Perret-Gentil, 4, Genève 14, 1211, Switzerland
Georg Ehret
Robertson Centre, University of Glasgow, Boyd Orr Building, Glasgow, G12 8QQ, Scotland
Ian Ford
Division of Endocrinology, Brigham and Women's Hospital and Harvard Medical School, 75 Francis St, Boston, 02115, Massachusetts, USA
Caroline S. Fox
Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Ferdinand-Sauerbruch-Str. NK, Greifswald, 17475, Germany
Nele Friedrich
Division of Biostatistics, Washington University, 660 S Euclid, St Louis, 63110, Missouri, USA
Charles Gu
Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, Edinburgh, UK
Chris Haley
National Institutes on Aging, National Institutes of Health, Bethesda, 20892, Maryland, USA
Tamara B. Harris & Lenore J. Launer
Department of Neurology, Boston University School of Medicine, 72 E Concord St, Boston, 02118, Massachusetts, USA
Nancy L. Heard-Costa & Sudha Seshadri
Department of Public Health, University of Helsinki, Hjelt Institute, P.O.Box 41, Mannerheimintie 172, Helsinki, FI-00014, Finland
Kauko Heikkilä, Anu Loukola, Eero Vuoksimaa & Jaakko Kaprio
Division of Applied Medicine, Musculoskeletal Research Programme, University of Aberdeen, Foresterhill, AB25 2ZD, Aberdeen, UK
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State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui Jin Hospital Affiliated with Shanghai Jiao Tong University School of Medicine, 197 Rui Jin Er Road, Shanghai, 200025, China
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Department of Radiology, Erasmus Medical Center, PO Box 2040, Rotterdam, 3000, CA, The Netherlands
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Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, SE-17121, Sweden
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Uppsala Clinical Research Center, Uppsala University, Uppsala, SE-75237, Sweden
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Department of Chronic Disease Prevention, National Institute for Health and Welfare, P.O. Box 30, Helsinki, FI-00271, Finland
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Department of Cardiology C5-P, Leiden University Medical Center, PO Box 9600, Leiden, 2300 RC, The Netherlands
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Department of Clinical Physiology, University of Tampere and Tampere University Hospital, P.O. Box 2000, Tampere, FI-33521, Finland
Mika Kähönen
Diabetes Prevention Unit, National Institute for Health and Welfare, P.O. Box 30, Helsinki, FI-00271, Finland
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Department of Medicine, Division of Endocrinology, Helsinki University Central Hospital, P.O.Box 340, Haartmaninkatu 4, Helsinki, FI-00029, Finland
Heikki A. Koistinen & Kirsi Pietilainen
Minerva Foundation Institute for Medical Research, Biomedicum 2U, Tukholmankatu 8, Helsinki, FI-00290, Finland
Heikki A. Koistinen
Laboratory for Genotyping Development RCfIMS, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Kanagawa, Japan
Michiaki Kubo
Department of Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, FI-70210, Finland
Johanna Kuusisto & Markku Laakso
Institute of Behavioural Sciences, University of Helsinki, P.O. Box 9, University of Helsinki, Helsinki, FI-00014, Finland
Jari Lahti
Folkhälsan Reasearch Centre, PB 63, Helsinki, FI-00014 University of Helsinki, Finland
Jari Lahti
Department of Clinical Chemistry, Fimlab Laboratories and School of Medicine University of Tampere, Tampere, FI-33520, Finland
Terho Lehtimäki
Department of Medical Sciences, University Hospital, Uppsala, 75185, Sweden
Lars Lind
Transplantation laboratory, Haartman Institute, University of Helsinki, P.O. Box 21, Helsinki, FI-00014, Finland
Marja-Liisa Lokki & Efthymia Vlachopoulou
Department of Health and Human Services, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, 27709, USA
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Ophthalmology, Massachusetts Eye and Ear, 243 Charles Street, Boston, 02114, Massachusetts, USA
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Department of Statistics, University of Auckland, 303.325 Science Centre, Private Bag 92019, Auckland, 1142, New Zealand
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Department of Health, Functional Capacity and Welfare, National Institute for Health and Welfare, P.O. Box 30, Helsinki, FI-00271, Finland
Annamari Lundqvist, Harri Rissanen & Paul Knekt
Department of Internal Medicine, University Hospital, Rue du Bugnon 44, Lausanne, 1011, Switzerland
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Human Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1HH, UK
Angela Matchan, Nicole Soranzo, Lorraine Southam & Eleftheria Zeggini
Division of Allergy and Clinical Immunology, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, 21224, Maryland, USA
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Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
Koichi Matsuda
Division of General Internal Medicine, Massachusetts General Hospital, 50 Staniford St, Boston, 02114, Massachusetts, USA
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Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, Neuherberg, 85764, Germany
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Institute of Human Genetics, Klinikum rechts der Isar, Technische Universität München, Ismaninger Str. 22, München, 81675, Germany
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Molecular Epidemiology, QIMR Berghofer Medical Research Institute, 300 Herston Rd, Herston, Brisbane, 4006, Queensland, Australia
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Genome Science Institute, Boston University School of Medicine, 72 East Concord Street, E-304, Boston, 02118, Massachusetts, USA
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HUCH Heart and Lung center, Helsinki University Central Hospital, P.O. Box 340, Helsinki, FI-00029, Finland
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Pulmonary Center and Department of Medicine, Boston University School of Medicine, 72 E Concord St, Boston, 02118, Massachusetts, USA
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Department of Medicine, University of Ibadan, Ibadan, Nigeria
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ICAMS, University of Glasgow, 126 University Way, Glasgow, G12 8TA, UK
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Division of Epidemiology and Community Health, University of Minnesota, 1300 S 2nd Street, Minneapolis, 55454, Minnesota, USA
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Centre for Global Health and Department of Public Health, School of Medicine, University of Split, Soltanska 2, Split, 21000, Croatia
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Obesity Research Unit, Research Programs Unit, Diabetes and Obesity, University of Helsinki, P.O.Box 63, Haartmaninkatu 8, Helsinki, FI-00014, Finland
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International Centre for Circulatory Health, Imperial College London, London, W2 1LA, UK
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Department of Cardiology and Cardio thoracic Surgery Hero DMC Heart Institute, Civil Lines, Ludhiana, 141001, India
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Department Public Health Sciences, University of Virginia School of Medicine, 3232 West Complex, Charlottesville, 22908, Virginia, USA
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Department of Psychological & Brain Sciences, Indiana University Bloomington, 1101 E. 10th Street, Bloomington, 47405, Indiana, USA
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University of Dundee, Kirsty Semple Way, Dundee, DD2 4DB, UK
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Division of Cardiology, Cardiovascular Health Research Unit, University of Washington, 1730 Minor Ave, Suite 1360, Seattle, 98101, Washington, USA
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Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, St. Stephen's Green, Dublin 2, Ireland
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UMR INSERM U1122,
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IGE-PCV “Interactions Gène-Environnement en Physiopathologie Cardio-Vasculaire”, INSERM, University of Lorraine, 30 Rue Lionnois, Nancy, 54000, France
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National Heart and Lung Institute, Imperial College London, Du Cane Road, London, W12 0NN, UK
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Department of Public Health Sciences, Stritch School of Medicine, Loyola University Chicago, Maywood, 60153, Illinois, USA
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NIHR Leicester Cardiovascular Biomedical Research Unit, University of Leicester, Glenfield Hospital, Groby Road, Leicester, LE3 9QP, UK
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Institute of Molecular and Cell Biology, University of Tartu, Riia 23, Tartu, 51010, Estonia
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Centre for Vascular Prevention, Danube-University Krems, Krems, 3500, Austria
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Diabetes Research Group, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
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Department of Internal Medicine, Erasmus Medical Center, PO Box 2040, Rotterdam, 3000, CA, The Netherlands
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Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, 21205, Maryland, USA
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Finnish Lung Health Association, Sibeliuksenkatu 11 A 1, Helsinki, FI-00250, Finland
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Genetic Epidemiology, QIMR Berghofer Medical Research Institute, 300 Herston Rd, Herston, Brisbane, 4006, Queensland, Australia
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Diabetes Unit, KEM Hospital and Research Centre, Rasta Peth, Pune, 411011, India.,
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Department of Medicine, Renal Unit, University of Verona, Piazzale A. Stefani 1, Verona, 37124, Italy
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Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, 44106, Ohio, USA
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Department of Medicine, Stanford University, 300 Pasteur Drive, Stanford, 94305, California, USA
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Translational Gerontology Branch, National institute on Aging, Baltimore, 21225, Maryland, USA
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Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, No. 9 Edinburgh Bioquarter, 9 Little France Road, Edinburgh, EH16 4UX, UK
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Centre for Pharmacogenetics and Pharmacogenomics, Medical Research Institute, University of Dundee, Ninewells Hospital and School of Medicine, Dundee, DD1 9SY, UK
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Department of Epidemiology, University of Alabama at Birmingham, 1665 University Boulevard, Birmingham, 35294, Alabama, USA
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Epidemiology of diabetes, obesity and chronic kidney disease over the lifecourse, Inserm, CESP Center for Research in Epidemiology and Population Health U1018, 16 Avenue Paul Vaillant Couturier, 94807 Villejuif, France
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Dipartimento di Scienze Mediche, Catholic University of the Sacred Heart, Via G. Moscati 31/34, Roma, 00168, Italy
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Department of Biostatistics, University of Liverpool, Duncan Building, Daulby Stree, Liverpool, L69 3GA, UK
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Department of General Practice and Primary Health Care, University of Helsinki, P.O. Box 20, University of Helsinki, Helsinki, FI-00014, Finland
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Vasa Central Hospital, Sandviksgatan 2-4, Vasa, FI-65130, Finland
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Folkhälsan Reasearch Centre, PB 63, University of Helsinki, Helsinki, FI-00014, Finland
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Unit of General Practice, Helsinki University Central Hospital, Haartmaninkatu 4, Helsinki, FI-00290, Finland
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Neuro-Imaging Genetics, QIMR Berghofer Medical Research Institute, 300 Herston Rd, Herston, Brisbane, 4006, Queensland, Australia
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Cardiovascular Genetics Division, University of Utah, 420 Chipeta Way, Room 1160, Salt Lake City, 84117, Utah, USA
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Alzheimer Scotland Research Centre, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
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Department of Psychiatry, Erasmus Medical Center, PO Box 2040, Rotterdam, 3000, CA, The Netherlands
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National Institute for Health and Welfare (THL), P.O.Box 30, Mannerheimintie 166, Helsinki, FI-00271, Finland
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Department of Kinesiology, Laval University, 2300 rue de la Terrasse, Quebec, G1V 0A6, Canada
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Department of Physiology and Biophysics, University of Mississippi Medical Center, 2500 N. State Street, Jackson, 39216, Mississippi, USA
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Department of Clinical Physiology and Nuclear Medicine, University of Turku and Turku University Hospital, Turku, FI-20521, Finland
Olli Raitakari
Research Center of Applied and Preventive Cardiovascular medicine, University of Turku, Turku, FI-20521, Finland
Olli Raitakari
Department of Genetics, University of Groningen, University Medical Center Groningen, Hanzeplein 1, Groningen, 9700 RB, The Netherlands
Pim van der Harst
Department of Economics, Stockholm School of Economics, Box 6501, Stockholm, SE-113 83, Sweden
Magnus Johannesson
Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Box 281, Stockholm, SE-171 77, Sweden
Patrik K. E. Magnusson
Department of Genetics and Biostatistics, Washington University School of Medicine, 4444 Forest Park Boulevard, Saint Louis, 63108, Missouri, USA
Ingrid B. Borecki
Department of Health Policy and Management, Johns Hopkins Bloomberg School of Public Health, Baltimore, 21205, Maryland, USA
Diane M. Becker
Department of Pediatrics, University of Oklahoma Health Sciences Center, 940 Stanton Young Boulevard, Oklahoma City, 73104, Oklahoma, USA
Dharambir K. Sanghera
Department of Pharmaceutical Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, 73104, Oklahoma, USA
Dharambir K. Sanghera
Sidra Medical and Research Centre, Doha, Qatar
Paolo Gasparini
The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, 10029, New York, USA
Ruth J. F. Loos
Genome Institute of Singapore, 60 Biopolis Street, #02-01 Genome, 138672, Singapore, Singapore
Giriraj R. Chandak
Department of Medicine, Program for Personalised and Genomic Medicine, University of Maryland School of Medicine, 685 Baltimore St. MSTF, Baltimore, 21201, Maryland, USA
Alan R. Shuldiner
Geriatric Research and Education Clinical Center, Veterans Administration Medical Center, 685 W Baltimore MSTF, Baltimore, 21201, Maryland, USA
Alan R. Shuldiner
BHF Glasgow Cardiovascular Research Centre, University of Glasgow, 126 University Place, Glasgow, G12 8TA, UK
Naveed Sattar
Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, 137 E. Franklin Street, Suite 306, Chapel Hill, 27599, North Carolina, USA
Kari E. North
Departments of Medicine, Cardiovascular Health Research Unit, Epidemiology and Health Services, University of Washington, 1730 Minor Ave, Suite 1360, Seattle, 98101, Washington, USA
Bruce M. Psaty
Group Health Research Institute, Group Health Cooperative, 1730 Minor Ave, Suite 1360, Seattle, 98101, Washington, USA
Bruce M. Psaty
Imperial College Healthcare NHS Trust, Imperial College London, Praed Street, London, W2 1NY, UK
John C. Chambers & Jaspal S. Kooner
Population Health Research Institute, St George's, University of London, Cranmer Terrace, London, SW17 0RE, UK
David P. Strachan
Steno Diabetes Centre, Niels Steensens Vej 2, Gentofte, 2820, Denmark
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Translational Laboratory in Genetic Medicine (TLGM), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, 138648, Singapore
Marie Loh
Centre for Population Health Sciences, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, UK
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Institutes for Neurogenetics and Integrative & Experimental Genomics, University of Lübeck, Lübeck, 23562, Germany
Lars Bertram
School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India
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