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Mahajan A, Taliun D, Thurner M, Robertson NR, Torres JM, Rayner NW, Steinthorsdottir V, Scott RA, Grarup N, Cook JP, Schmidt EM, Wuttke M, Sarnowski C, Mägi R, Nano J, Gieger C, Trompet S, Lecoeur C, Preuss M, Prins BP, Guo X, Bielak LF, Bennett AJ, Bork-Jensen J, Brummett CM, Canouil M, Eckardt KU, Fischer K, Kardia SLR, Kronenberg F, Läll K, Liu CT, Locke AE, Luan J, Ntalla I, Nylander V, Schönherr S, Schurmann C, Yengo L, Bottinger EP, Brandslund I, Christensen C, Dedoussis G, Florez JC, ford I, Franco OH, Frayling TM, Giedraitis V, Hackinger S, Hattersley AT, Herder C, Ikram MA, Ingelsson M, Jørgensen ME, Jørgensen T, Kriebel J, Kuusisto J, Ligthart S, Lindgren CM, Linneberg A, Lyssenko V, Mamakou V, Meitinger T, Mohlke KL, Morris AD, Nadkarni G, Pankow JS, Peters A, Sattar N, Stančáková A, Strauch K, Taylor KD, Thorand B, Thorleifsson G, Thorsteinsdottir U, Tuomilehto J, Witte DR, Dupuis J, Peyser PA, Zeggini E, Loos RJF, Froguel P, Ingelsson E, Lind L, Groop L, Laakso M, Collins FS, Jukema JW, Palmer CNA, Grallert H, Metspalu A, Dehghan A, Köttgen A, Abecasis G, Meigs JB, Rotter JI, Marchini J, Pedersen O, Hansen T, Langenberg C, Wareham NJ, Stefansson K, Gloyn AL, Morris AP, Boehnke M, McCarthy MI. Fine-mapping type 2 diabetes loci to single-variant resolution using high-density imputation and islet-specific epigenome maps. Nat Genet 2018; 50:1505-1513. [PMID: 30297969 PMCID: PMC6287706 DOI: 10.1038/s41588-018-0241-6] [Citation(s) in RCA: 1028] [Impact Index Per Article: 171.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Accepted: 08/10/2018] [Indexed: 12/30/2022]
Abstract
We expanded GWAS discovery for type 2 diabetes (T2D) by combining data from 898,130 European-descent individuals (9% cases), after imputation to high-density reference panels. With these data, we (i) extend the inventory of T2D-risk variants (243 loci, 135 newly implicated in T2D predisposition, comprising 403 distinct association signals); (ii) enrich discovery of lower-frequency risk alleles (80 index variants with minor allele frequency <5%, 14 with estimated allelic odds ratio >2); (iii) substantially improve fine-mapping of causal variants (at 51 signals, one variant accounted for >80% posterior probability of association (PPA)); (iv) extend fine-mapping through integration of tissue-specific epigenomic information (islet regulatory annotations extend the number of variants with PPA >80% to 73); (v) highlight validated therapeutic targets (18 genes with associations attributable to coding variants); and (vi) demonstrate enhanced potential for clinical translation (genome-wide chip heritability explains 18% of T2D risk; individuals in the extremes of a T2D polygenic risk score differ more than ninefold in prevalence).
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Affiliation(s)
- Anubha Mahajan
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
| | - Daniel Taliun
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Matthias Thurner
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 7LE, UK
| | - Neil R Robertson
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 7LE, UK
| | - Jason M Torres
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
| | - N William Rayner
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 7LE, UK
- Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | | | - Robert A Scott
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Niels Grarup
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
| | - James P Cook
- Department of Biostatistics, University of Liverpool, Liverpool, L69 3GA, UK
| | - Ellen M Schmidt
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Matthias Wuttke
- Institute of Genetic Epidemiology, Medical Center – University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, 79106, Germany
| | - Chloé Sarnowski
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, 02118, USA
| | - Reedik Mägi
- Estonian Genome Center, University of Tartu, Tartu, 51010, Estonia
| | - Jana Nano
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, 3015CN, The Netherlands
| | - Christian Gieger
- Research Unit of Molecular Epidemiology, Institute of Epidemiology 2, Helmholtz Zentrum München, German Research Center for Environmental Health, München-Neuherberg, Germany
- German Center for Diabetes Research (DZD), München-Neuherberg, Germany
| | - Stella Trompet
- Section of Gerontology and Geriatrics, Department of Internal Medicine, Leiden University Medical Center, Leiden, 2300 RC, the Netherlands
- Department of Cardiology, Leiden University Medical Center, Leiden, 2300 RC, the Netherlands
| | - Cécile Lecoeur
- CNRS-UMR8199, Lille University, Lille Pasteur Institute, Lille, 59000, France
| | - Michael Preuss
- The Charles Bronfman Institute for Personalized Medicine, The Icahn School of Medicine at Mount Sinai, New York, 10029, USA
| | - Bram Peter Prins
- Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Xiuqing Guo
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, LABioMed at Harbor-UCLA Medical Center, Torrance, California, 90502, US
| | - Lawrence F Bielak
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | | | - Amanda J Bennett
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 7LE, UK
| | - Jette Bork-Jensen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Chad M Brummett
- Department of Anesthesiology, University of Michigan Medical School, Ann Arbor, MI, 48109, US
| | - Mickaël Canouil
- CNRS-UMR8199, Lille University, Lille Pasteur Institute, Lille, 59000, France
| | - Kai-Uwe Eckardt
- Department of Nephrology and Medical Intensive Care Charité, University Medicine Berlin, Berlin, 10117, Germany and German Chronic Kidney Disease study
| | - Krista Fischer
- Estonian Genome Center, University of Tartu, Tartu, 51010, Estonia
| | - Sharon LR Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Florian Kronenberg
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, 6020, Austria and German Chronic Kidney Disease study
| | - Kristi Läll
- Estonian Genome Center, University of Tartu, Tartu, 51010, Estonia
- Institute of Mathematical Statistics, University of Tartu, Tartu, Estonia
| | - Ching-Ti Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, 02118, USA
| | - Adam E Locke
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Division of Genomics & Bioinformatics, Washington University School of Medicine, St. Louis, MO, USA
| | - Jian'an Luan
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Ioanna Ntalla
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Vibe Nylander
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 7LE, UK
| | - Sebastian Schönherr
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, 6020, Austria and German Chronic Kidney Disease study
| | - Claudia Schurmann
- The Charles Bronfman Institute for Personalized Medicine, The Icahn School of Medicine at Mount Sinai, New York, 10029, USA
| | - Loïc Yengo
- CNRS-UMR8199, Lille University, Lille Pasteur Institute, Lille, 59000, France
| | - Erwin P Bottinger
- The Charles Bronfman Institute for Personalized Medicine, The Icahn School of Medicine at Mount Sinai, New York, 10029, USA
| | - Ivan Brandslund
- Institute of Regional Health Research, University of Southern Denmark, Odense, 5000, Denmark
- Department of Clinical Biochemistry, Vejle Hospital, Vejle, 7100, Denmark
| | | | - George Dedoussis
- Department of Nutrition and Dietetics, Harokopio University of Athens, Athens, 17671, Greece
| | - Jose C Florez
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, 02115, USA
- Diabetes Research Center (Diabetes Unit), Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, 02114, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute, Cambridge, MA, 02142, USA
| | - Ian ford
- Robertson Centre for Biostatistics, University of Glasgow, Glasgow, UK
| | - Oscar H Franco
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, 3015CN, The Netherlands
| | - Timothy M Frayling
- Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, EX1 2LU, UK
| | - Vilmantas Giedraitis
- Department of Public Health and Caring Sciences, Geriatrics, Uppsala University, Uppsala, SE-751 85, Sweden
| | - Sophie Hackinger
- Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Andrew T Hattersley
- University of Exeter Medical School, University of Exeter, Exeter, EX2 5DW, UK
| | - Christian Herder
- German Center for Diabetes Research (DZD), München-Neuherberg, Germany
- Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, 3015CN, The Netherlands
| | - Martin Ingelsson
- Department of Public Health and Caring Sciences, Geriatrics, Uppsala University, Uppsala, SE-751 85, Sweden
| | - Marit E Jørgensen
- Steno Diabetes Center Copenhagen, Gentofte, 2820, Denmark
- National Institute of Public Health, Southern Denmark University, Copenhagen, 1353, Denmark
| | - Torben Jørgensen
- Research Centre for Prevention and Health, Capital Region of Denmark, Glostrup, 2600, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Faculty of Medicine, Aalborg University, Aalborg, Denmark
| | - Jennifer Kriebel
- Research Unit of Molecular Epidemiology, Institute of Epidemiology II, Helmholtz Zentrum München Research Center for Environmental Health, Neuherberg, 85764, Germany
- German Center for Diabetes Research (DZD), Neuherberg, 85764, Germany
| | - Johanna Kuusisto
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, 70210, Finland
| | - Symen Ligthart
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, 3015CN, The Netherlands
| | - Cecilia M Lindgren
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, 02142, USA
- Big Data Institute, Li Ka Shing Centre For Health Information and Discovery, University of Oxford, Oxford, OX37BN, UK
| | - Allan Linneberg
- Research Centre for Prevention and Health, Capital Region of Denmark, Glostrup, 2600, Denmark
- Department of Clinical Experimental Research, Rigshospitalet, Glostrup, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Valeriya Lyssenko
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University Diabetes Centre, Malmö, 20502, Sweden
| | - Vasiliki Mamakou
- Dromokaiteio Psychiatric Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Thomas Meitinger
- Institute of Human Genetics, Technische Universität München, Munich, 81675, Germany
- Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, 85764, Germany
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, 27599, USA
| | - Andrew D Morris
- Clinical Research Centre, Centre for Molecular Medicine, Ninewells Hospital and Medical School, Dundee, DD1 9SY, UK
- The Usher Institute to the Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, EH16 4UX, UK
| | - Girish Nadkarni
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10069, USA
| | - James S Pankow
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, 55454, US
| | - Annette Peters
- German Center for Diabetes Research (DZD), Neuherberg, 85764, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, 81675, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, 85764, Germany
| | - Naveed Sattar
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, G12 8TA, UK
| | - Alena Stančáková
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, 70210, Finland
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, 85764, Germany
- Institute of Medical Informatics, Biometry and Epidemiology, Chair of Genetic Epidemiology, Ludwig-Maximilians-Universität, Munich, 80802, Germany
| | - Kent D Taylor
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, LABioMed at Harbor-UCLA Medical Center, Torrance, California, 90502, US
| | - Barbara Thorand
- German Center for Diabetes Research (DZD), Neuherberg, 85764, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, 85764, Germany
| | | | - Unnur Thorsteinsdottir
- deCODE Genetics, Amgen inc., Reykjavik, 101, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, 101, Iceland
| | - Jaakko Tuomilehto
- Department of Health, National Institute for Health and Welfare, Helsinki, 00271, Finland
- Dasman Diabetes Institute, Dasman, 15462, Kuwait
- Department of Neuroscience and Preventive Medicine, Danube-University Krems, Krems, 3500, Austria
- Diabetes Research Group, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Daniel R Witte
- Department of Public Health, Aarhus University, Aarhus, Denmark
- Danish Diabetes Academy, Odense, Denmark
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, 02118, USA
- National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, Massachusetts, 01702, USA
| | - Patricia A Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Eleftheria Zeggini
- Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, The Icahn School of Medicine at Mount Sinai, New York, 10029, USA
- Mindich Child Health and Development Institute, The Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Philippe Froguel
- CNRS-UMR8199, Lille University, Lille Pasteur Institute, Lille, 59000, France
- Department of Genomics of Common Disease, School of Public Health, Imperial College London, London, W12 0NN, UK
| | - Erik Ingelsson
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, 94305, US
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, 75185, Sweden
| | - Lars Lind
- Department of Medical Sciences, Uppsala University, Uppsala, SE-751 85, Sweden
| | - Leif Groop
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University Diabetes Centre, Malmö, 20502, Sweden
- Finnish Institute for Molecular Medicine (FIMM), University of Helsinki, Helsinki, Finland
| | - Markku Laakso
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, 70210, Finland
| | - Francis S Collins
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - J Wouter Jukema
- Department of Cardiology, Leiden University Medical Center, Leiden, 2300 RC, the Netherlands
| | - Colin N A Palmer
- Pat Macpherson Centre for Pharmacogenetics and Pharmacogenomics, Ninewells Hospital and Medical School, University of Dundee, Dundee, DD1 9SY, UK
| | - Harald Grallert
- Research Unit of Molecular Epidemiology, Institute of Epidemiology II, Helmholtz Zentrum München Research Center for Environmental Health, Neuherberg, 85764, Germany
- German Center for Diabetes Research (DZD), Neuherberg, 85764, Germany
- Clinical Cooparation Group Type 2 Diabetes, Helmholtz Zentrum München, Ludwig-Maximillians University Munich, Germany
- Clinical Cooparation Group Nutrigenomics and Type 2 Diabetes, Helmholtz Zentrum München, Technical University Munich, Germany
| | - Andres Metspalu
- Estonian Genome Center, University of Tartu, Tartu, 51010, Estonia
| | - Abbas Dehghan
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, 3015CN, The Netherlands
- Department of Epidemiology and Biostatistics, Imperial College London, London, W2 1PG, UK
- MRC-PHE Centre for Environment and Health, Imperial College London, London, W2 1PG, UK
| | - Anna Köttgen
- Institute of Genetic Epidemiology, Medical Center – University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, 79106, Germany
| | - Goncalo Abecasis
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - James B Meigs
- General Medicine Division, Massachusetts General Hospital and Department of Medicine, Harvard Medical School, Boston, Massachusetts, 02114, USA
| | - Jerome I Rotter
- Departments of Pediatrics and Medicine, The Institute for Translational Genomics and Population Sciences, LABioMed at Harbor-UCLA Medical Center, Torrance, California, 90502, US
| | - Jonathan Marchini
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
- Department of Statistics, University of Oxford, Oxford, OX1 3TG, UK
| | - Oluf Pedersen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Torben Hansen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
- Faculty of Health Sciences, University of Southern Denmark, Odense, 5000, Denmark
| | - Claudia Langenberg
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Nicholas J Wareham
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Kari Stefansson
- deCODE Genetics, Amgen inc., Reykjavik, 101, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, 101, Iceland
| | - Anna L Gloyn
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 7LE, UK
- Oxford NIHR Biomedical Research Centre, Oxford University Hospitals Trust, Oxford, OX3 7LE, UK
| | - Andrew P Morris
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
- Department of Biostatistics, University of Liverpool, Liverpool, L69 3GA, UK
- Estonian Genome Center, University of Tartu, Tartu, 51010, Estonia
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Mark I McCarthy
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 7LE, UK
- Oxford NIHR Biomedical Research Centre, Oxford University Hospitals Trust, Oxford, OX3 7LE, UK
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