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Scott RA, Scott LJ, Mägi R, Marullo L, Gaulton KJ, Kaakinen M, Pervjakova N, Pers TH, Johnson AD, Eicher JD, Jackson AU, Ferreira T, Lee Y, Ma C, Steinthorsdottir V, Thorleifsson G, Qi L, Van Zuydam NR, Mahajan A, Chen H, Almgren P, Voight BF, Grallert H, Müller-Nurasyid M, Ried JS, Rayner NW, Robertson N, Karssen LC, van Leeuwen EM, Willems SM, Fuchsberger C, Kwan P, Teslovich TM, Chanda P, Li M, Lu Y, Dina C, Thuillier D, Yengo L, Jiang L, Sparso T, Kestler HA, Chheda H, Eisele L, Gustafsson S, Frånberg M, Strawbridge RJ, Benediktsson R, Hreidarsson AB, Kong A, Sigurðsson G, Kerrison ND, Luan J, Liang L, Meitinger T, Roden M, Thorand B, Esko T, Mihailov E, Fox C, Liu CT, Rybin D, Isomaa B, Lyssenko V, Tuomi T, Couper DJ, Pankow JS, Grarup N, Have CT, Jørgensen ME, Jørgensen T, Linneberg A, Cornelis MC, van Dam RM, Hunter DJ, Kraft P, Sun Q, Edkins S, Owen KR, Perry JRB, Wood AR, Zeggini E, Tajes-Fernandes J, Abecasis GR, Bonnycastle LL, Chines PS, Stringham HM, Koistinen HA, Kinnunen L, Sennblad B, Mühleisen TW, Nöthen MM, Pechlivanis S, Baldassarre D, Gertow K, Humphries SE, Tremoli E, Klopp N, Meyer J, Steinbach G, Wennauer R, Eriksson JG, Mӓnnistö S, Peltonen L, Tikkanen E, Charpentier G, Eury E, Lobbens S, Gigante B, Leander K, McLeod O, Bottinger EP, Gottesman O, Ruderfer D, Blüher M, Kovacs P, Tonjes A, Maruthur NM, Scapoli C, Erbel R, Jöckel KH, Moebus S, de Faire U, Hamsten A, Stumvoll M, Deloukas P, Donnelly PJ, Frayling TM, Hattersley AT, Ripatti S, Salomaa V, Pedersen NL, Boehm BO, Bergman RN, Collins FS, Mohlke KL, Tuomilehto J, Hansen T, Pedersen O, Barroso I, Lannfelt L, Ingelsson E, Lind L, Lindgren CM, Cauchi S, Froguel P, Loos RJF, Balkau B, Boeing H, Franks PW, Barricarte Gurrea A, Palli D, van der Schouw YT, Altshuler D, Groop LC, Langenberg C, Wareham NJ, Sijbrands E, van Duijn CM, Florez JC, Meigs JB, Boerwinkle E, Gieger C, Strauch K, Metspalu A, Morris AD, Palmer CNA, Hu FB, Thorsteinsdottir U, Stefansson K, Dupuis J, Morris AP, Boehnke M, McCarthy MI, Prokopenko I. An Expanded Genome-Wide Association Study of Type 2 Diabetes in Europeans. Diabetes 2017; 66:2888-2902. [PMID: 28566273 PMCID: PMC5652602 DOI: 10.2337/db16-1253] [Citation(s) in RCA: 456] [Impact Index Per Article: 65.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 05/21/2017] [Indexed: 12/12/2022]
Abstract
To characterize type 2 diabetes (T2D)-associated variation across the allele frequency spectrum, we conducted a meta-analysis of genome-wide association data from 26,676 T2D case and 132,532 control subjects of European ancestry after imputation using the 1000 Genomes multiethnic reference panel. Promising association signals were followed up in additional data sets (of 14,545 or 7,397 T2D case and 38,994 or 71,604 control subjects). We identified 13 novel T2D-associated loci (P < 5 × 10-8), including variants near the GLP2R, GIP, and HLA-DQA1 genes. Our analysis brought the total number of independent T2D associations to 128 distinct signals at 113 loci. Despite substantially increased sample size and more complete coverage of low-frequency variation, all novel associations were driven by common single nucleotide variants. Credible sets of potentially causal variants were generally larger than those based on imputation with earlier reference panels, consistent with resolution of causal signals to common risk haplotypes. Stratification of T2D-associated loci based on T2D-related quantitative trait associations revealed tissue-specific enrichment of regulatory annotations in pancreatic islet enhancers for loci influencing insulin secretion and in adipocytes, monocytes, and hepatocytes for insulin action-associated loci. These findings highlight the predominant role played by common variants of modest effect and the diversity of biological mechanisms influencing T2D pathophysiology.
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Affiliation(s)
- Robert A Scott
- MRC Epidemiology Unit, University of Cambridge, Cambridge, U.K
| | - Laura J Scott
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI
| | - Reedik Mägi
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Letizia Marullo
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Kyle J Gaulton
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, U.K
- Department of Genetics, Stanford University, Stanford, CA
| | - Marika Kaakinen
- Department of Genomics of Common Disease, Imperial College London, London, U.K
| | | | - Tune H Pers
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Division of Endocrinology and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Andrew D Johnson
- Framingham Heart Study, Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, Framingham, MA
| | - John D Eicher
- Framingham Heart Study, Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, Framingham, MA
| | - Anne U Jackson
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI
| | - Teresa Ferreira
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, U.K
| | - Yeji Lee
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI
| | - Clement Ma
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI
| | | | | | - Lu Qi
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Natalie R Van Zuydam
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, U.K
- Pat Macpherson Centre for Pharmacogenetics and Pharmacogenomics and Biomedical Research Institute, Ninewells Hospital, University of Dundee, Dundee, U.K
| | - Anubha Mahajan
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, U.K
| | - Han Chen
- Human Genetics Center and Department of Epidemiology, Human Genetics & Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX
- Center for Precision Health, School Biomedical Informatics, and School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX
| | - Peter Almgren
- Lund University Diabetes Centre and Department of Clinical Sciences Malmö, University Hospital Scania, Lund University, Malmö, Sweden
| | - Ben F Voight
- Department of Pharmacology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- Institute of Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Harald Grallert
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research, Neuherberg, Germany
| | - Martina Müller-Nurasyid
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Department of Medicine I, University Hospital Grosshadern, Ludwig-Maximilians-Universität, Munich, Germany
- Genetic Epidemiology, Institute of Medical Informatics, Biometry and Epidemiology, Ludwig-Maximilians-Universität, Munich, Germany
- Munich Heart Alliance, German Centre for Cardiovascular Disease, Munich, Germany
| | - Janina S Ried
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Nigel W Rayner
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, U.K
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, U.K
- Wellcome Trust Sanger Institute, Hinxton, U.K
| | - Neil Robertson
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, U.K
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, U.K
| | - Lennart C Karssen
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
- PolyOmica, 's-Hertogenbosch, the Netherlands
| | | | - Sara M Willems
- MRC Epidemiology Unit, University of Cambridge, Cambridge, U.K
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Christian Fuchsberger
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI
| | - Phoenix Kwan
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI
| | - Tanya M Teslovich
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI
| | - Pritam Chanda
- High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Man Li
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | - Yingchang Lu
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
- The Genetics of Obesity and Related Metabolic Traits Program, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Christian Dina
- l'institut du thorax, INSERM, CNRS, Centre Hospitalier Universitaire de Nantes, Université de Nantes, Nantes, France
| | - Dorothee Thuillier
- Lille Institute of Biology, European Genomics Institute of Diabetes, Lille, France
- CNRS UMR 8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, University of Lille, Lille, France
| | - Loic Yengo
- Lille Institute of Biology, European Genomics Institute of Diabetes, Lille, France
- CNRS UMR 8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, University of Lille, Lille, France
| | - Longda Jiang
- Department of Genomics of Common Disease, Imperial College London, London, U.K
| | - Thomas Sparso
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Hans A Kestler
- Leibniz Institute on Aging, Fritz Lipmann Institute, Jena, Germany
- Institute of Medical Systems Biology, Ulm University, Ulm, Germany
| | - Himanshu Chheda
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Lewin Eisele
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital of Essen, Essen, Germany
| | - Stefan Gustafsson
- Molecular Epidemiology, Department of Medical Sciences, and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Mattias Frånberg
- Cardiovascular Medicine Unit, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Stockholm, Sweden
- Department for Numerical Analysis and Computer Science, Stockholm University, Stockholm, Sweden
| | - Rona J Strawbridge
- Cardiovascular Medicine Unit, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Rafn Benediktsson
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
- Landspítali University Hospital, Reykjavik, Iceland
| | | | | | - Gunnar Sigurðsson
- Landspítali University Hospital, Reykjavik, Iceland
- Icelandic Heart Association, Kópavogur, Iceland
| | | | - Jian'an Luan
- MRC Epidemiology Unit, University of Cambridge, Cambridge, U.K
| | - Liming Liang
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Thomas Meitinger
- Munich Heart Alliance, German Centre for Cardiovascular Disease, Munich, Germany
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
- Institute of Human Genetics, Technische Universität München, Munich, Germany
| | - Michael Roden
- German Center for Diabetes Research, Neuherberg, Germany
- Department of Endocrinology and Diabetology, Medical Faculty, Heinrich-Heine University, Düsseldorf, Germany
- Institute for Clinical Diabetology, German Diabetes Center, Leibniz Institute for Diabetes Research at Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Barbara Thorand
- Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research, Neuherberg, Germany
| | - Tõnu Esko
- Estonian Genome Center, University of Tartu, Tartu, Estonia
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Division of Genetics and Endocrinology, Boston Children's Hospital, Boston, MA
| | | | - Caroline Fox
- Framingham Heart Study, National Heart, Lung, and Blood Institute, Framingham, MA
- Division of Endocrinology, Diabetes and Hypertension, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Ching-Ti Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | - Denis Rybin
- Data Coordinating Center, Boston University School of Public Health, Boston, MA
| | - Bo Isomaa
- Folkhälsan Research Center, Helsinki, Finland
- Department of Social Services and Health Care, Jakobstad, Finland
| | - Valeriya Lyssenko
- Lund University Diabetes Centre and Department of Clinical Sciences Malmö, University Hospital Scania, Lund University, Malmö, Sweden
| | - Tiinamaija Tuomi
- Folkhälsan Research Center, Helsinki, Finland
- Department of Medicine, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - David J Couper
- Collaborative Studies Coordinating Center, Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - James S Pankow
- Division of Epidemiology & Community Health, University of Minnesota, Minneapolis, MN
| | - Niels Grarup
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Christian T Have
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Torben Jørgensen
- Research Centre for Prevention and Health, Capital Region of Denmark, Copenhagen, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Faculty of Medicine, Aalborg University, Aalborg, Denmark
| | - Allan Linneberg
- Research Centre for Prevention and Health, Capital Region of Denmark, Copenhagen, Denmark
- Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Marilyn C Cornelis
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Rob M van Dam
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - David J Hunter
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Peter Kraft
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Qi Sun
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | | | - Katharine R Owen
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, U.K
- National Institute for Health Research Oxford Biomedical Research Centre, Churchill Hospital, Oxford, U.K
| | - John R B Perry
- MRC Epidemiology Unit, University of Cambridge, Cambridge, U.K
| | - Andrew R Wood
- Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, U.K
| | | | | | - Goncalo R Abecasis
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI
| | - Lori L Bonnycastle
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Peter S Chines
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Heather M Stringham
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI
| | - Heikki A Koistinen
- Department of Health, National Institute for Health and Welfare, Helsinki, Finland
- Endocrinology, Department of Medicine and Abdominal Center, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, Biomedicum Helsinki 2U, Helsinki, Finland
| | - Leena Kinnunen
- Department of Health, National Institute for Health and Welfare, Helsinki, Finland
- Endocrinology, Department of Medicine and Abdominal Center, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, Biomedicum Helsinki 2U, Helsinki, Finland
| | - Bengt Sennblad
- Cardiovascular Medicine Unit, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Stockholm, Sweden
| | - Thomas W Mühleisen
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Sonali Pechlivanis
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital of Essen, Essen, Germany
| | - Damiano Baldassarre
- Centro Cardiologico Monzino, Istituto di Ricovero e Cura a Carattere Scientifico, Milan, Italy
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università di Milano, Milan, Italy
| | - Karl Gertow
- Cardiovascular Medicine Unit, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Steve E Humphries
- Cardiovascular Genetics, BHF Laboratories, Institute Cardiovascular Sciences, University College London, London, U.K
| | - Elena Tremoli
- Centro Cardiologico Monzino, Istituto di Ricovero e Cura a Carattere Scientifico, Milan, Italy
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università di Milano, Milan, Italy
| | - Norman Klopp
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Hannover Unified Biobank, Hannover Medical School, Hannover, Germany
| | - Julia Meyer
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Gerald Steinbach
- Department of Clinical Chemistry and Central Laboratory, University of Ulm, Ulm, Germany
| | - Roman Wennauer
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Johan G Eriksson
- Folkhälsan Research Center, Helsinki, Finland
- Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland
- Department of General Practice and Primary Health Care, University of Helsinki, Helsinki, Finland
- Unit of General Practice, Helsinki University Central Hospital, Helsinki, Finland
| | - Satu Mӓnnistö
- Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland
| | - Leena Peltonen
- Wellcome Trust Sanger Institute, Hinxton, U.K
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Emmi Tikkanen
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- Department of Public Health, Hjelt Institute, University of Helsinki, Helsinki, Finland
| | | | - Elodie Eury
- CNRS UMR 8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, University of Lille, Lille, France
| | - Stéphane Lobbens
- CNRS UMR 8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, University of Lille, Lille, France
| | - Bruna Gigante
- Division of Cardiovascular Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Karin Leander
- Division of Cardiovascular Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Olga McLeod
- Cardiovascular Medicine Unit, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Erwin P Bottinger
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Omri Gottesman
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Douglas Ruderfer
- Division of Psychiatric Genomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Matthias Blüher
- IFB AdiposityDiseases, University of Leipzig, Leipzig, Germany
- Department of Medicine, University of Leipzig, Leipzig, Germany
| | - Peter Kovacs
- IFB AdiposityDiseases, University of Leipzig, Leipzig, Germany
- Department of Medicine, University of Leipzig, Leipzig, Germany
| | - Anke Tonjes
- IFB AdiposityDiseases, University of Leipzig, Leipzig, Germany
- Department of Medicine, University of Leipzig, Leipzig, Germany
| | - Nisa M Maruthur
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
- Division of General Internal Medicine, Department of Medicine, Johns Hopkins Bloomberg School of Medicine, Baltimore, MD
- The Welch Center for Prevention, Epidemiology and Clinical Research, Johns Hopkins University, Baltimore, MD
| | - Chiara Scapoli
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Raimund Erbel
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital of Essen, Essen, Germany
| | - Karl-Heinz Jöckel
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital of Essen, Essen, Germany
| | - Susanne Moebus
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital of Essen, Essen, Germany
| | - Ulf de Faire
- Division of Cardiovascular Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Anders Hamsten
- Cardiovascular Medicine Unit, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Michael Stumvoll
- IFB AdiposityDiseases, University of Leipzig, Leipzig, Germany
- Department of Medicine, University of Leipzig, Leipzig, Germany
| | - Panagiotis Deloukas
- Wellcome Trust Sanger Institute, Hinxton, U.K
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University London, London, U.K
| | - Peter J Donnelly
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, U.K
- Department of Statistics, University of Oxford, Oxford, U.K
| | - Timothy M Frayling
- Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, U.K
| | - Andrew T Hattersley
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, U.K
| | - Samuli Ripatti
- Wellcome Trust Sanger Institute, Hinxton, U.K
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- Department of Public Health, Hjelt Institute, University of Helsinki, Helsinki, Finland
- Public Health Genomics Unit, National Institute for Health and Welfare, Helsinki, Finland
| | - Veikko Salomaa
- Department of Health, National Institute for Health and Welfare, Helsinki, Finland
| | - Nancy L Pedersen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Bernhard O Boehm
- Division of Endocrinology and Diabetes, Department of Internal Medicine, University Medical Centre Ulm, Ulm, Germany
- Lee Kong Chian School of Medicine, Imperial College London and Nanyang Technological University, Singapore, Singapore
| | - Richard N Bergman
- Diabetes and Obesity Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Francis S Collins
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, NC
| | - Jaakko Tuomilehto
- Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland
- Dasman Diabetes Institute, Dasman, Kuwait
- Centre for Vascular Prevention, Danube University Krems, Krems, Austria
- Diabetes Research Group, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
| | - Oluf Pedersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Inês Barroso
- Wellcome Trust Sanger Institute, Hinxton, U.K
- University of Cambridge Metabolic Research Laboratories and National Institute for Health Research Cambridge Biomedical Research Centre, Wellcome Trust-MRC Institute of Metabolic Science, Addenbrooke's Hospital Cambridge, Cambridge, U.K
| | - Lars Lannfelt
- Department of Public Health and Caring Sciences, Uppsala University, Uppsala, Sweden
| | - Erik Ingelsson
- Molecular Epidemiology, Department of Medical Sciences, and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA
| | - Lars Lind
- Cardiovascular Epidemiology, Department of Medical Sciences, Uppsala University Hospital, Uppsala, Sweden
| | - Cecilia M Lindgren
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, U.K
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Stephane Cauchi
- Lille Institute of Biology, European Genomics Institute of Diabetes, Lille, France
| | - Philippe Froguel
- Department of Genomics of Common Disease, Imperial College London, London, U.K
- Lille Institute of Biology, European Genomics Institute of Diabetes, Lille, France
- CNRS UMR 8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, University of Lille, Lille, France
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
- The Genetics of Obesity and Related Metabolic Traits Program, Icahn School of Medicine at Mount Sinai, New York, NY
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Beverley Balkau
- INSERM, CESP, UMR 1018, Villejuif, France
- University of Paris-Sud, UMR 1018, Villejuif, France
| | - Heiner Boeing
- German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
| | - Paul W Franks
- Lund University, Malmö, Sweden
- Umeå University, Umeå, Sweden
| | - Aurelio Barricarte Gurrea
- Navarra Public Health Institute, Pamplona, Spain
- Navarra Institute for Health Research, Pamplona, Spain
- CIBER Epidemiology and Public Health, Madrid, Spain
| | - Domenico Palli
- Cancer Research and Prevention Institute, Florence, Italy
| | | | - David Altshuler
- Broad Institute of MIT and Harvard, Cambridge, MA
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
- Department of Genetics, Harvard Medical School, Boston, MA
- Department of Molecular Biology, Harvard Medical School, Boston, MA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA
| | - Leif C Groop
- Lund University Diabetes Centre and Department of Clinical Sciences Malmö, University Hospital Scania, Lund University, Malmö, Sweden
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | | | | | - Eric Sijbrands
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Cornelia M van Duijn
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
- Netherlands Genomics Initiative, Netherlands Consortium for Healthy Ageing and Center for Medical Systems Biology, Rotterdam, the Netherlands
| | - Jose C Florez
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Department of Medicine, Harvard Medical School, Boston, MA
- Diabetes Unit and Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA
| | - James B Meigs
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Department of Medicine, Harvard Medical School, Boston, MA
- General Medicine Division, Massachusetts General Hospital, Boston, MA
| | - Eric Boerwinkle
- Human Genetics Center, The University of Texas Health Science Center at Houston, Houston, TX
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Christian Gieger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Genetic Epidemiology, Institute of Medical Informatics, Biometry and Epidemiology, Ludwig-Maximilians-Universität, Munich, Germany
| | - Andres Metspalu
- Estonian Genome Center, University of Tartu, Tartu, Estonia
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Andrew D Morris
- Usher Institute of Population Health Sciences and Informatics, The University of Edinburgh, Edinburgh, U.K
| | - Colin N A Palmer
- Pat Macpherson Centre for Pharmacogenetics and Pharmacogenomics and Biomedical Research Institute, Ninewells Hospital, University of Dundee, Dundee, U.K
- Cardiovascular and Diabetes Medicine, Biomedical Research Institute, Ninewells Hospital, University of Dundee, Dundee, U.K
| | - Frank B Hu
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Unnur Thorsteinsdottir
- deCODE genetics, Amgen, Inc., Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Kari Stefansson
- deCODE genetics, Amgen, Inc., Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Josée Dupuis
- Framingham Heart Study, National Heart, Lung, and Blood Institute, Framingham, MA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | - Andrew P Morris
- Estonian Genome Center, University of Tartu, Tartu, Estonia
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, U.K
- Department of Biostatistics, University of Liverpool, Liverpool, U.K
- Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, U.K
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI
| | - Mark I McCarthy
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, U.K.
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, U.K
- National Institute for Health Research Oxford Biomedical Research Centre, Churchill Hospital, Oxford, U.K
| | - Inga Prokopenko
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, U.K.
- Department of Genomics of Common Disease, Imperial College London, London, U.K
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, U.K
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Perilli G, Di Battista B, Montana A, Pavia J, Cauchi S, Zerafa NM, Pomara C. A rare case of a scuba diver's death due to propeller injuries of a desalination pump. J Forensic Leg Med 2015; 32:21-4. [PMID: 25882144 DOI: 10.1016/j.jflm.2015.02.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 02/07/2015] [Indexed: 11/18/2022]
Abstract
Water skiing, boat racing, skin and scuba diving, as well as pleasure boat cruising are becoming increasingly popular hobbies. As a result, the incidence of injuries secondary to motor propellers is becoming more frequent. Injuries by propellers, amputation, death by drowning, and bleeding are rare reported events in forensic literature. The most common circumstances surrounding boat-propeller-related injuries are concerned with getting into or out of the boat, personal watercraft use or water skiing, and falling or being thrown from the boat. A case of a scuba diver's death that occurred during an illegal scuba fishing trip around a desalination plant is presented. A complete autopsy and histological study of all organs and surfaces of dismembered cadaveric sections, performed in order to determine the phases of death, are reported. An underwater scene investigation was conducted by an engineering team studying the mouth of the pump and the dynamic characteristic of rotating propeller blades.
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Affiliation(s)
- G Perilli
- Department of Forensic Pathology, University of Foggia, Ospedale Colonnello d'Avanzo, Viale degli Aviatori 1, 71100 Foggia, Italy
| | - B Di Battista
- Department of Forensic Pathology, University of Foggia, Ospedale Colonnello d'Avanzo, Viale degli Aviatori 1, 71100 Foggia, Italy
| | - A Montana
- Department of Forensic Toxicology "G.F. Ingrassia", University of Catania, via S. Sofia 87, Comparto 10, 95123, Catania, Italy
| | - J Pavia
- Department of Anatomy, University of Malta, Msida, Malta
| | - S Cauchi
- Department of Anatomy, University of Malta, Msida, Malta
| | - N M Zerafa
- Department of Anatomy, University of Malta, Msida, Malta
| | - C Pomara
- Department of Forensic Pathology, University of Foggia, Ospedale Colonnello d'Avanzo, Viale degli Aviatori 1, 71100 Foggia, Italy; Department of Anatomy, University of Malta, Msida, Malta.
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3
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Mahajan A, Go MJ, Zhang W, Below JE, Gaulton KJ, Ferreira T, Horikoshi M, Johnson AD, Ng MCY, Prokopenko I, Saleheen D, Wang X, Zeggini E, Abecasis GR, Adair LS, Almgren P, Atalay M, Aung T, Baldassarre D, Balkau B, Bao Y, Barnett AH, Barroso I, Basit A, Been LF, Beilby J, Bell GI, Benediktsson R, Bergman RN, Boehm BO, Boerwinkle E, Bonnycastle LL, Burtt N, Cai Q, Campbell H, Carey J, Cauchi S, Caulfield M, Chan JCN, Chang LC, Chang TJ, Chang YC, Charpentier G, Chen CH, Chen H, Chen YT, Chia KS, Chidambaram M, Chines PS, Cho NH, Cho YM, Chuang LM, Collins FS, Cornelis MC, Couper DJ, Crenshaw AT, van Dam RM, Danesh J, Das D, de Faire U, Dedoussis G, Deloukas P, Dimas AS, Dina C, Doney AS, Donnelly PJ, Dorkhan M, van Duijn C, Dupuis J, Edkins S, Elliott P, Emilsson V, Erbel R, Eriksson JG, Escobedo J, Esko T, Eury E, Florez JC, Fontanillas P, Forouhi NG, Forsen T, Fox C, Fraser RM, Frayling TM, Froguel P, Frossard P, Gao Y, Gertow K, Gieger C, Gigante B, Grallert H, Grant GB, Grrop LC, Groves CJ, Grundberg E, Guiducci C, Hamsten A, Han BG, Hara K, Hassanali N, Hattersley AT, Hayward C, Hedman AK, Herder C, Hofman A, Holmen OL, Hovingh K, Hreidarsson AB, Hu C, Hu FB, Hui J, Humphries SE, Hunt SE, Hunter DJ, Hveem K, Hydrie ZI, Ikegami H, Illig T, Ingelsson E, Islam M, Isomaa B, Jackson AU, Jafar T, James A, Jia W, Jöckel KH, Jonsson A, Jowett JBM, Kadowaki T, Kang HM, Kanoni S, Kao WHL, Kathiresan S, Kato N, Katulanda P, Keinanen-Kiukaanniemi KM, Kelly AM, Khan H, Khaw KT, Khor CC, Kim HL, Kim S, Kim YJ, Kinnunen L, Klopp N, Kong A, Korpi-Hyövälti E, Kowlessur S, Kraft P, Kravic J, Kristensen MM, Krithika S, Kumar A, Kumate J, Kuusisto J, Kwak SH, Laakso M, Lagou V, Lakka TA, Langenberg C, Langford C, Lawrence R, Leander K, Lee JM, Lee NR, Li M, Li X, Li Y, Liang J, Liju S, Lim WY, Lind L, Lindgren CM, Lindholm E, Liu CT, Liu JJ, Lobbens S, Long J, Loos RJF, Lu W, Luan J, Lyssenko V, Ma RCW, Maeda S, Mägi R, Männisto S, Matthews DR, Meigs JB, Melander O, Metspalu A, Meyer J, Mirza G, Mihailov E, Moebus S, Mohan V, Mohlke KL, Morris AD, Mühleisen TW, Müller-Nurasyid M, Musk B, Nakamura J, Nakashima E, Navarro P, Ng PK, Nica AC, Nilsson PM, Njølstad I, Nöthen MM, Ohnaka K, Ong TH, Owen KR, Palmer CNA, Pankow JS, Park KS, Parkin M, Pechlivanis S, Pedersen NL, Peltonen L, Perry JRB, Peters A, Pinidiyapathirage JM, Platou CG, Potter S, Price JF, Qi L, Radha V, Rallidis L, Rasheed A, Rathman W, Rauramaa R, Raychaudhuri S, Rayner NW, Rees SD, Rehnberg E, Ripatti S, Robertson N, Roden M, Rossin EJ, Rudan I, Rybin D, Saaristo TE, Salomaa V, Saltevo J, Samuel M, Sanghera DK, Saramies J, Scott J, Scott LJ, Scott RA, Segrè AV, Sehmi J, Sennblad B, Shah N, Shah S, Shera AS, Shu XO, Shuldiner AR, Sigurđsson G, Sijbrands E, Silveira A, Sim X, Sivapalaratnam S, Small KS, So WY, Stančáková A, Stefansson K, Steinbach G, Steinthorsdottir V, Stirrups K, Strawbridge RJ, Stringham HM, Sun Q, Suo C, Syvänen AC, Takayanagi R, Takeuchi F, Tay WT, Teslovich TM, Thorand B, Thorleifsson G, Thorsteinsdottir U, Tikkanen E, Trakalo J, Tremoli E, Trip MD, Tsai FJ, Tuomi T, Tuomilehto J, Uitterlinden AG, Valladares-Salgado A, Vedantam S, Veglia F, Voight BF, Wang C, Wareham NJ, Wennauer R, Wickremasinghe AR, Wilsgaard T, Wilson JF, Wiltshire S, Winckler W, Wong TY, Wood AR, Wu JY, Wu Y, Yamamoto K, Yamauchi T, Yang M, Yengo L, Yokota M, Young R, Zabaneh D, Zhang F, Zhang R, Zheng W, Zimmet PZ, Altshuler D, Bowden DW, Cho YS, Cox NJ, Cruz M, Hanis CL, Kooner J, Lee JY, Seielstad M, Teo YY, Boehnke M, Parra EJ, Chambers JC, Tai ES, McCarthy MI, Morris AP. Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility. Nat Genet 2014; 46:234-44. [PMID: 24509480 PMCID: PMC3969612 DOI: 10.1038/ng.2897] [Citation(s) in RCA: 777] [Impact Index Per Article: 77.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Accepted: 01/17/2014] [Indexed: 11/18/2022]
Abstract
To further understanding of the genetic basis of type 2 diabetes (T2D) susceptibility, we aggregated published meta-analyses of genome-wide association studies (GWAS) including 26,488 cases and 83,964 controls of European, East Asian, South Asian, and Mexican and Mexican American ancestry. We observed significant excess in directional consistency of T2D risk alleles across ancestry groups, even at SNPs demonstrating only weak evidence of association. By following up the strongest signals of association from the trans-ethnic meta-analysis in an additional 21,491 cases and 55,647 controls of European ancestry, we identified seven novel T2D susceptibility loci. Furthermore, we observed considerable improvements in fine-mapping resolution of common variant association signals at several T2D susceptibility loci. These observations highlight the benefits of trans-ethnic GWAS for the discovery and characterisation of complex trait loci, and emphasize an exciting opportunity to extend insight into the genetic architecture and pathogenesis of human diseases across populations of diverse ancestry.
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Charpentier G, Balkau B, Benhamou P, Cauchi S, Cosson E, Fontaine P, Froguel P, Gourdy P, Guerci B, Hebel P, Mistretta F, Jeandidier N, Penfornis A, Raccah D, Reznik Y, Scheen A, Canipel L. Premiers enseignements de l’étude DESCENDANCE : prévalence des dysglycémies méconnues chez des apparentés de diabétiques de type 2 sur deux générations. Rev Epidemiol Sante Publique 2014. [DOI: 10.1016/j.respe.2013.11.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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Baerenwald DA, Bonnefond A, Bouatia-Naji N, Flemming BP, Umunakwe OC, Oeser JK, Pound LD, Conley NL, Cauchi S, Lobbens S, Eury E, Balkau B, Lantieri O, Dadi PK, Jacobson DA, Froguel P, O’Brien RM. Multiple functional polymorphisms in the G6PC2 gene contribute to the association with higher fasting plasma glucose levels. Diabetologia 2013; 56:1306-16. [PMID: 23508304 PMCID: PMC4106008 DOI: 10.1007/s00125-013-2875-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Accepted: 01/28/2013] [Indexed: 01/14/2023]
Abstract
AIMS/HYPOTHESIS We previously identified the G6PC2 locus as a strong determinant of fasting plasma glucose (FPG) and showed that a common G6PC2 intronic single nucleotide polymorphism (SNP) (rs560887) and two common G6PC2 promoter SNPs (rs573225 and rs13431652) are highly associated with FPG. However, these promoter SNPs have complex effects on G6PC2 fusion gene expression, and our data suggested that only rs13431652 is a potentially causative SNP. Here we examine the effect of rs560887 on G6PC2 pre-mRNA splicing and the contribution of an additional common G6PC2 promoter SNP, rs2232316, to the association signal. METHODS Minigene analyses were used to characterise the effect of rs560887 on G6PC2 pre-mRNA splicing. Fusion gene and gel retardation analyses characterised the effect of rs2232316 on G6PC2 promoter activity and transcription factor binding. The genetic association of rs2232316 with FPG variation was assessed using regression adjusted for age, sex and BMI in 4,220 Europeans with normal FPG. RESULTS The rs560887-G allele was shown to enhance G6PC2 pre-mRNA splicing, whereas the rs2232316-A allele enhanced G6PC2 transcription by promoting Foxa2 binding. Genetic analyses provide evidence for association of the rs2232316-A allele with increased FPG (β = 0.04 mmol/l; p = 4.3 × 10(-3)) as part of the same signal as rs560887, rs573225 and rs13431652. CONCLUSIONS/INTERPRETATION As with rs13431652, the in situ functional data with rs560887 and rs2232316 are in accord with the putative function of G6PC2 in pancreatic islets, and suggest that all three are potentially causative SNPs that contribute to the association between G6PC2 and FPG.
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Affiliation(s)
- D. A. Baerenwald
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, 37232 Nashville, Tennessee, USA
| | - A. Bonnefond
- CNRS-UMR-8199, Institut Pasteur de Lille, F-59019, Lille, France
- University Lille Nord de France, F-59019 Lille, France
| | - N. Bouatia-Naji
- CNRS-UMR-8199, Institut Pasteur de Lille, F-59019, Lille, France
- University Lille Nord de France, F-59019 Lille, France
- INSERM U970, Paris Cardiovascular Research Center PARCC, 56 rue Leblanc, F-75015 Paris, France
| | - B. P. Flemming
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, 37232 Nashville, Tennessee, USA
| | - O. C. Umunakwe
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, 37232 Nashville, Tennessee, USA
| | - J. K. Oeser
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, 37232 Nashville, Tennessee, USA
| | - L. D. Pound
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, 37232 Nashville, Tennessee, USA
| | - N. L. Conley
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, 37232 Nashville, Tennessee, USA
| | - S. Cauchi
- CNRS-UMR-8199, Institut Pasteur de Lille, F-59019, Lille, France
- University Lille Nord de France, F-59019 Lille, France
| | - S. Lobbens
- CNRS-UMR-8199, Institut Pasteur de Lille, F-59019, Lille, France
- University Lille Nord de France, F-59019 Lille, France
| | - E. Eury
- CNRS-UMR-8199, Institut Pasteur de Lille, F-59019, Lille, France
- University Lille Nord de France, F-59019 Lille, France
| | - B. Balkau
- INSERM, Centre for research in Epidemiology and Population Health (CESP), U1018, Epidemiology of diabetes, obesity and chronic renal disease over the lifecourse, F-94807, Villejuif, France
- Université Paris-Sud 11, UMRS 1018, F-94807 Villejuif, France
| | - O. Lantieri
- Institut inter-régional pour la santé (IRSA), F-37521 La Riche, France
| | - MAGIC Investigators
- Meta-Analysis of Glucose and Insulin related traits Consortium Investigators (http://www.magicinvestigators.org/)
| | - P. K. Dadi
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, 37232 Nashville, Tennessee, USA
| | - D. A. Jacobson
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, 37232 Nashville, Tennessee, USA
| | - P. Froguel
- CNRS-UMR-8199, Institut Pasteur de Lille, F-59019, Lille, France
- University Lille Nord de France, F-59019 Lille, France
- Department of Genomics of Common Disease, School of Public Health, Imperial College London, W12 0NN London, UK
- Correspondence should be addressed to either P.F. at Department of Genomics of Common Disease, School of Public Health, Imperial College London, W12 0NN London, UK () or R.O’B at Department of Molecular Physiology and Biophysics, 8415 MRB IV, 2213 Garland Ave, Vanderbilt University School of Medicine, Nashville, TN 37232-0615, USA ()
| | - R. M. O’Brien
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, 37232 Nashville, Tennessee, USA
- Correspondence should be addressed to either P.F. at Department of Genomics of Common Disease, School of Public Health, Imperial College London, W12 0NN London, UK () or R.O’B at Department of Molecular Physiology and Biophysics, 8415 MRB IV, 2213 Garland Ave, Vanderbilt University School of Medicine, Nashville, TN 37232-0615, USA ()
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6
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Albrechtsen A, Grarup N, Li Y, Sparsø T, Tian G, Cao H, Jiang T, Kim SY, Korneliussen T, Li Q, Nie C, Wu R, Skotte L, Morris AP, Ladenvall C, Cauchi S, Stančáková A, Andersen G, Astrup A, Banasik K, Bennett AJ, Bolund L, Charpentier G, Chen Y, Dekker JM, Doney ASF, Dorkhan M, Forsen T, Frayling TM, Groves CJ, Gui Y, Hallmans G, Hattersley AT, He K, Hitman GA, Holmkvist J, Huang S, Jiang H, Jin X, Justesen JM, Kristiansen K, Kuusisto J, Lajer M, Lantieri O, Li W, Liang H, Liao Q, Liu X, Ma T, Ma X, Manijak MP, Marre M, Mokrosiński J, Morris AD, Mu B, Nielsen AA, Nijpels G, Nilsson P, Palmer CNA, Rayner NW, Renström F, Ribel-Madsen R, Robertson N, Rolandsson O, Rossing P, Schwartz TW, Slagboom PE, Sterner M, Tang M, Tarnow L, Tuomi T, van’t Riet E, van Leeuwen N, Varga TV, Vestmar MA, Walker M, Wang B, Wang Y, Wu H, Xi F, Yengo L, Yu C, Zhang X, Zhang J, Zhang Q, Zhang W, Zheng H, Zhou Y, Altshuler D, ‘t Hart LM, Franks PW, Balkau B, Froguel P, McCarthy MI, Laakso M, Groop L, Christensen C, Brandslund I, Lauritzen T, Witte DR, Linneberg A, Jørgensen T, Hansen T, Wang J, Nielsen R, Pedersen O. Exome sequencing-driven discovery of coding polymorphisms associated with common metabolic phenotypes. Diabetologia 2013; 56:298-310. [PMID: 23160641 PMCID: PMC3536959 DOI: 10.1007/s00125-012-2756-1] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2012] [Accepted: 09/28/2012] [Indexed: 12/13/2022]
Abstract
AIMS/HYPOTHESIS Human complex metabolic traits are in part regulated by genetic determinants. Here we applied exome sequencing to identify novel associations of coding polymorphisms at minor allele frequencies (MAFs) >1% with common metabolic phenotypes. METHODS The study comprised three stages. We performed medium-depth (8×) whole exome sequencing in 1,000 cases with type 2 diabetes, BMI >27.5 kg/m(2) and hypertension and in 1,000 controls (stage 1). We selected 16,192 polymorphisms nominally associated (p < 0.05) with case-control status, from four selected annotation categories or from loci reported to associate with metabolic traits. These variants were genotyped in 15,989 Danes to search for association with 12 metabolic phenotypes (stage 2). In stage 3, polymorphisms showing potential associations were genotyped in a further 63,896 Europeans. RESULTS Exome sequencing identified 70,182 polymorphisms with MAF >1%. In stage 2 we identified 51 potential associations with one or more of eight metabolic phenotypes covered by 45 unique polymorphisms. In meta-analyses of stage 2 and stage 3 results, we demonstrated robust associations for coding polymorphisms in CD300LG (fasting HDL-cholesterol: MAF 3.5%, p = 8.5 × 10(-14)), COBLL1 (type 2 diabetes: MAF 12.5%, OR 0.88, p = 1.2 × 10(-11)) and MACF1 (type 2 diabetes: MAF 23.4%, OR 1.10, p = 8.2 × 10(-10)). CONCLUSIONS/INTERPRETATION We applied exome sequencing as a basis for finding genetic determinants of metabolic traits and show the existence of low-frequency and common coding polymorphisms with impact on common metabolic traits. Based on our study, coding polymorphisms with MAF above 1% do not seem to have particularly high effect sizes on the measured metabolic traits.
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Affiliation(s)
- A. Albrechtsen
- Centre of Bioinformatics, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - N. Grarup
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, DIKU Building, Universitetsparken 1, 2100 Copenhagen Ø, Denmark
| | - Y. Li
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, 518083 Shenzhen, China
| | - T. Sparsø
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, DIKU Building, Universitetsparken 1, 2100 Copenhagen Ø, Denmark
| | | | - H. Cao
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, 518083 Shenzhen, China
| | - T. Jiang
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, 518083 Shenzhen, China
| | - S. Y. Kim
- Department of Integrative Biology, University of California, 3060 Valley Life Sciences, Bldg #3140, Berkeley, CA 94720-3140 USA
| | - T. Korneliussen
- Centre of Bioinformatics, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Q. Li
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, 518083 Shenzhen, China
| | - C. Nie
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, 518083 Shenzhen, China
| | - R. Wu
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, 518083 Shenzhen, China
| | - L. Skotte
- Centre of Bioinformatics, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - A. P. Morris
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - C. Ladenvall
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University and Lund University Diabetes Centre, Malmö, Sweden
| | - S. Cauchi
- UMR CNRS 8199, Genomic and Metabolic Disease, Lille, France
| | - A. Stančáková
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - G. Andersen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, DIKU Building, Universitetsparken 1, 2100 Copenhagen Ø, Denmark
| | - A. Astrup
- Department of Human Nutrition, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - K. Banasik
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, DIKU Building, Universitetsparken 1, 2100 Copenhagen Ø, Denmark
| | - A. J. Bennett
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
| | - L. Bolund
- Institute of Human Genetics, Aarhus University, Aarhus, Denmark
| | - G. Charpentier
- Department of Endocrinology-Diabetology, Corbeil-Essonnes Hospital, Corbeil-Essonnes, France
| | - Y. Chen
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, 518083 Shenzhen, China
| | - J. M. Dekker
- EMGO Institute for Health and Care Research, VU University Medical Center, Amsterdam, the Netherlands
| | - A. S. F. Doney
- Diabetes Research Centre, Biomedical Research Institute, University of Dundee, Ninewells Hospital, Dundee, UK
- Pharmacogenomics Centre, Biomedical Research Institute, University of Dundee, Ninewells Hospital, Dundee, UK
| | - M. Dorkhan
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University and Lund University Diabetes Centre, Malmö, Sweden
| | - T. Forsen
- Department of General Practice and Primary Health Care, University of Helsinki, Helsinki, Finland
- Vasa Health Care Center, Vaasa, Finland
| | - T. M. Frayling
- Genetics of Complex Traits, Institute of Biomedical and Clinical Science, Peninsula Medical School, University of Exeter, Exeter, UK
- Diabetes Genetics, Institute of Biomedical and Clinical Science, Peninsula Medical School, University of Exeter, Exeter, UK
| | - C. J. Groves
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
| | - Y. Gui
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, 518083 Shenzhen, China
| | - G. Hallmans
- Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
| | - A. T. Hattersley
- Genetics of Complex Traits, Institute of Biomedical and Clinical Science, Peninsula Medical School, University of Exeter, Exeter, UK
- Diabetes Genetics, Institute of Biomedical and Clinical Science, Peninsula Medical School, University of Exeter, Exeter, UK
| | - K. He
- Chinese PLA General Hospital, Beijing, China
| | - G. A. Hitman
- Centre for Diabetes, Blizard Institute, Queen Mary University of London, London, UK
| | - J. Holmkvist
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, DIKU Building, Universitetsparken 1, 2100 Copenhagen Ø, Denmark
- Vipergen Aps, Copenhagen, Denmark
| | - S. Huang
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, 518083 Shenzhen, China
- School of Bioscience and Biotechnology, South China University of Technology, Guangzhou, China
| | - H. Jiang
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, 518083 Shenzhen, China
| | - X. Jin
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, 518083 Shenzhen, China
| | - J. M. Justesen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, DIKU Building, Universitetsparken 1, 2100 Copenhagen Ø, Denmark
| | - K. Kristiansen
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - J. Kuusisto
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - M. Lajer
- Steno Diabetes Center, Gentofte, Denmark
| | - O. Lantieri
- Institut inter Regional pour la Santé (IRSA), La Riche, France
| | - W. Li
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, 518083 Shenzhen, China
| | - H. Liang
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, 518083 Shenzhen, China
| | - Q. Liao
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, 518083 Shenzhen, China
| | - X. Liu
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, 518083 Shenzhen, China
| | - T. Ma
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, 518083 Shenzhen, China
| | - X. Ma
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, 518083 Shenzhen, China
| | - M. P. Manijak
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, DIKU Building, Universitetsparken 1, 2100 Copenhagen Ø, Denmark
| | - M. Marre
- Department of Endocrinology, Diabetology and Nutrition, Bichat-Claude Bernard University Hospital, Assistance Publique des Hôpitaux de Paris, Paris, France
- Inserm U695, Université Denis Diderot Paris 7, Paris, France
| | - J. Mokrosiński
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, DIKU Building, Universitetsparken 1, 2100 Copenhagen Ø, Denmark
- Laboratory for Molecular Pharmacology, Department of Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - A. D. Morris
- Diabetes Research Centre, Biomedical Research Institute, University of Dundee, Ninewells Hospital, Dundee, UK
- Pharmacogenomics Centre, Biomedical Research Institute, University of Dundee, Ninewells Hospital, Dundee, UK
| | - B. Mu
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, 518083 Shenzhen, China
| | - A. A. Nielsen
- Department of Clinical Biochemistry, Vejle Hospital, Vejle, Denmark
| | - G. Nijpels
- EMGO Institute for Health and Care Research, VU University Medical Center, Amsterdam, the Netherlands
| | - P. Nilsson
- Department of Clinical Sciences, Medicine, Lund University, Malmö, Sweden
| | - C. N. A. Palmer
- Diabetes Research Centre, Biomedical Research Institute, University of Dundee, Ninewells Hospital, Dundee, UK
- Pharmacogenomics Centre, Biomedical Research Institute, University of Dundee, Ninewells Hospital, Dundee, UK
| | - N. W. Rayner
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
| | - F. Renström
- Department of Clinical Sciences, Genetic and Molecular Epidemiology Unit, Skåna University Hospital, Lund University, Malmö, Sweden
| | - R. Ribel-Madsen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, DIKU Building, Universitetsparken 1, 2100 Copenhagen Ø, Denmark
| | - N. Robertson
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
| | - O. Rolandsson
- Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
| | - P. Rossing
- Steno Diabetes Center, Gentofte, Denmark
| | - T. W. Schwartz
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, DIKU Building, Universitetsparken 1, 2100 Copenhagen Ø, Denmark
- Laboratory for Molecular Pharmacology, Department of Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - P. E. Slagboom
- Section of Molecular Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
- Netherlands Center for Healthy Ageing, Leiden, the Netherlands
| | - M. Sterner
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University and Lund University Diabetes Centre, Malmö, Sweden
| | | | - M. Tang
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, 518083 Shenzhen, China
| | - L. Tarnow
- Steno Diabetes Center, Gentofte, Denmark
| | | | - T. Tuomi
- Department of Medicine, Helsinki University Hospital, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
| | - E. van’t Riet
- EMGO Institute for Health and Care Research, VU University Medical Center, Amsterdam, the Netherlands
| | - N. van Leeuwen
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - T. V. Varga
- Department of Clinical Sciences, Genetic and Molecular Epidemiology Unit, Skåna University Hospital, Lund University, Malmö, Sweden
| | - M. A. Vestmar
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, DIKU Building, Universitetsparken 1, 2100 Copenhagen Ø, Denmark
- Laboratory for Molecular Pharmacology, Department of Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - M. Walker
- Diabetes Research Group, School of Clinical Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - B. Wang
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, 518083 Shenzhen, China
| | - Y. Wang
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, 518083 Shenzhen, China
| | - H. Wu
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, 518083 Shenzhen, China
| | - F. Xi
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, 518083 Shenzhen, China
| | - L. Yengo
- UMR CNRS 8199, Genomic and Metabolic Disease, Lille, France
| | - C. Yu
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, 518083 Shenzhen, China
| | - X. Zhang
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, 518083 Shenzhen, China
| | - J. Zhang
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, 518083 Shenzhen, China
| | - Q. Zhang
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, 518083 Shenzhen, China
| | - W. Zhang
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, 518083 Shenzhen, China
| | - H. Zheng
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, 518083 Shenzhen, China
| | - Y. Zhou
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, 518083 Shenzhen, China
| | - D. Altshuler
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA USA
- Broad Institute of Harvard and MIT, Cambridge, MA USA
| | - L. M. ‘t Hart
- Section of Molecular Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - P. W. Franks
- Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
- Department of Clinical Sciences, Genetic and Molecular Epidemiology Unit, Skåna University Hospital, Lund University, Malmö, Sweden
- Department of Nutrition, Harvard School of Public Health, Boston, MA USA
| | - B. Balkau
- Inserm CESP U1018, Villejuif, France
| | - P. Froguel
- UMR CNRS 8199, Genomic and Metabolic Disease, Lille, France
- Genomic Medicine, Hammersmith Hospital, Imperial College London, London, UK
| | - M. I. McCarthy
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
- Oxford National Institute for Health Research Biomedical Research Centre, Churchill Hospital, Oxford, UK
| | - M. Laakso
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - L. Groop
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University and Lund University Diabetes Centre, Malmö, Sweden
| | - C. Christensen
- Department of Internal Medicine and Endocrinology, Vejle Hospital, Vejle, Denmark
| | - I. Brandslund
- Department of Clinical Biochemistry, Vejle Hospital, Vejle, Denmark
- Institute of Regional Health Research, University of Southern Denmark, Odense, Denmark
| | - T. Lauritzen
- Department of General Practice, Aarhus University, Aarhus, Denmark
| | | | - A. Linneberg
- Research Centre for Prevention and Health, Glostrup University Hospital, Glostrup, Denmark
| | - T. Jørgensen
- Research Centre for Prevention and Health, Glostrup University Hospital, Glostrup, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Faculty of Medicine, University of Aalborg, Aalborg, Denmark
| | - T. Hansen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, DIKU Building, Universitetsparken 1, 2100 Copenhagen Ø, Denmark
- Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
| | - J. Wang
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, DIKU Building, Universitetsparken 1, 2100 Copenhagen Ø, Denmark
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, 518083 Shenzhen, China
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - R. Nielsen
- Centre of Bioinformatics, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
- Department of Integrative Biology, University of California, 3060 Valley Life Sciences, Bldg #3140, Berkeley, CA 94720-3140 USA
- Department of Statistics, University of California, Berkeley, CA USA
| | - O. Pedersen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, DIKU Building, Universitetsparken 1, 2100 Copenhagen Ø, Denmark
- Faculty of Health Sciences, Aarhus University, Aarhus, Denmark
- Hagedorn Research Institute, Gentofte, Denmark
- Institute of Biomedical Science, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Beulens JWJ, van der Schouw YT, Bergmann MM, Rohrmann S, Schulze MB, Buijsse B, Grobbee DE, Arriola L, Cauchi S, Tormo MJ, Allen NE, van der A DL, Balkau B, Boeing H, Clavel-Chapelon F, de Lauzon-Guillan B, Franks P, Froguel P, Gonzales C, Halkjaer J, Huerta JM, Kaaks R, Key TJ, Khaw KT, Krogh V, Molina-Montes E, Nilsson P, Overvad K, Palli D, Panico S, Ramón Quirós J, Rolandsson O, Romieu I, Romaguera D, Sacerdote C, Sánchez MJ, Spijkerman AMW, Teucher B, Tjonneland A, Tumino R, Sharp S, Forouhi NG, Langenberg C, Feskens EJM, Riboli E, Wareham NJ. Alcohol consumption and risk of type 2 diabetes in European men and women: influence of beverage type and body size The EPIC-InterAct study. J Intern Med 2012; 272:358-70. [PMID: 22353562 DOI: 10.1111/j.1365-2796.2012.02532.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
OBJECTIVE To investigate the association between alcohol consumption and type 2 diabetes, and determine whether this is modified by sex, body mass index (BMI) and beverage type. DESIGN Multicentre prospective case-cohort study. SETTING Eight countries from the European Prospective Investigation into Cancer and Nutrition cohort. SUBJECTS A representative baseline sample of 16 154 participants and 12 403 incident cases of type 2 diabetes. INTERVENTIONS Alcohol consumption assessed using validated dietary questionnaires. MAIN OUTCOME MEASURES Occurrence of type 2 diabetes based on multiple sources (mainly self-reports), verified against medical information. RESULTS Amongst men, moderate alcohol consumption was nonsignificantly associated with a lower incidence of diabetes with a hazard ratio (HR) of 0.90 (95% CI: 0.78-1.05) for 6.1-12.0 versus 0.1-6.0 g day(-1) , adjusted for dietary and diabetes risk factors. However, the lowest risk was observed at higher intakes of 24.1-96.0 g day(-1) with an HR of 0.86 (95% CI: 0.75-0.98). Amongst women, moderate alcohol consumption was associated with a lower incidence of diabetes with a hazard ratio of 0.82 (95% CI: 0.72-0.92) for 6.1-12.0 g day(-1) (P interaction gender <0.01). The inverse association between alcohol consumption and diabetes was more pronounced amongst overweight (BMI ≥ 25 kg m(-2) ) than normal-weight men and women (P interaction < 0.05). Adjusting for waist and hip circumference did not alter the results for men, but attenuated the association for women (HR=0.90, 95% CI: 0.79-1.03 for 6.1-12.0 g day(-1) ). Wine consumption for men and fortified wine consumption for women were most strongly associated with a reduced risk of diabetes. CONCLUSIONS The results of this study show that moderate alcohol consumption is associated with a lower risk of type 2 diabetes amongst women only. However, this risk reduction is in part explained by fat distribution. The relation between alcohol consumption and type 2 diabetes was stronger for overweight than normal-weight women and men.
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Morris AP, Voight BF, Teslovich TM, Ferreira T, Segrè AV, Steinthorsdottir V, Strawbridge RJ, Khan H, Grallert H, Mahajan A, Prokopenko I, Kang HM, Dina C, Esko T, Fraser RM, Kanoni S, Kumar A, Lagou V, Langenberg C, Luan J, Lindgren CM, Müller-Nurasyid M, Pechlivanis S, Rayner NW, Scott LJ, Wiltshire S, Yengo L, Kinnunen L, Rossin EJ, Raychaudhuri S, Johnson AD, Dimas AS, Loos RJF, Vedantam S, Chen H, Florez JC, Fox C, Liu CT, Rybin D, Couper DJ, Kao WHL, Li M, Cornelis MC, Kraft P, Sun Q, van Dam RM, Stringham HM, Chines PS, Fischer K, Fontanillas P, Holmen OL, Hunt SE, Jackson AU, Kong A, Lawrence R, Meyer J, Perry JRB, Platou CGP, Potter S, Rehnberg E, Robertson N, Sivapalaratnam S, Stančáková A, Stirrups K, Thorleifsson G, Tikkanen E, Wood AR, Almgren P, Atalay M, Benediktsson R, Bonnycastle LL, Burtt N, Carey J, Charpentier G, Crenshaw AT, Doney ASF, Dorkhan M, Edkins S, Emilsson V, Eury E, Forsen T, Gertow K, Gigante B, Grant GB, Groves CJ, Guiducci C, Herder C, Hreidarsson AB, Hui J, James A, Jonsson A, Rathmann W, Klopp N, Kravic J, Krjutškov K, Langford C, Leander K, Lindholm E, Lobbens S, Männistö S, Mirza G, Mühleisen TW, Musk B, Parkin M, Rallidis L, Saramies J, Sennblad B, Shah S, Sigurðsson G, Silveira A, Steinbach G, Thorand B, Trakalo J, Veglia F, Wennauer R, Winckler W, Zabaneh D, Campbell H, van Duijn C, Uitterlinden AG, Hofman A, Sijbrands E, Abecasis GR, Owen KR, Zeggini E, Trip MD, Forouhi NG, Syvänen AC, Eriksson JG, Peltonen L, Nöthen MM, Balkau B, Palmer CNA, Lyssenko V, Tuomi T, Isomaa B, Hunter DJ, Qi L, Shuldiner AR, Roden M, Barroso I, Wilsgaard T, Beilby J, Hovingh K, Price JF, Wilson JF, Rauramaa R, Lakka TA, Lind L, Dedoussis G, Njølstad I, Pedersen NL, Khaw KT, Wareham NJ, Keinanen-Kiukaanniemi SM, Saaristo TE, Korpi-Hyövälti E, Saltevo J, Laakso M, Kuusisto J, Metspalu A, Collins FS, Mohlke KL, Bergman RN, Tuomilehto J, Boehm BO, Gieger C, Hveem K, Cauchi S, Froguel P, Baldassarre D, Tremoli E, Humphries SE, Saleheen D, Danesh J, Ingelsson E, Ripatti S, Salomaa V, Erbel R, Jöckel KH, Moebus S, Peters A, Illig T, de Faire U, Hamsten A, Morris AD, Donnelly PJ, Frayling TM, Hattersley AT, Boerwinkle E, Melander O, Kathiresan S, Nilsson PM, Deloukas P, Thorsteinsdottir U, Groop LC, Stefansson K, Hu F, Pankow JS, Dupuis J, Meigs JB, Altshuler D, Boehnke M, McCarthy MI. Large-scale association analysis provides insights into the genetic architecture and pathophysiology of type 2 diabetes. Nat Genet 2012; 44:981-90. [PMID: 22885922 PMCID: PMC3442244 DOI: 10.1038/ng.2383] [Citation(s) in RCA: 1413] [Impact Index Per Article: 117.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Accepted: 07/11/2012] [Indexed: 11/09/2022]
Abstract
To extend understanding of the genetic architecture and molecular basis of type 2 diabetes (T2D), we conducted a meta-analysis of genetic variants on the Metabochip, including 34,840 cases and 114,981 controls, overwhelmingly of European descent. We identified ten previously unreported T2D susceptibility loci, including two showing sex-differentiated association. Genome-wide analyses of these data are consistent with a long tail of additional common variant loci explaining much of the variation in susceptibility to T2D. Exploration of the enlarged set of susceptibility loci implicates several processes, including CREBBP-related transcription, adipocytokine signaling and cell cycle regulation, in diabetes pathogenesis.
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Affiliation(s)
- Andrew P Morris
- Wellcome Trust Centre for Human Genetics, University of Oxford, UK.
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9
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Cauchi S, Ezzidi I, El Achhab Y, Mtiraoui N, Chaieb L, Salah D, Nejjari C, Labrune Y, Yengo L, Beury D, Vaxillaire M, Mahjoub T, Chikri M, Froguel P. European genetic variants associated with type 2 diabetes in North African Arabs. Diabetes Metab 2012; 38:316-23. [PMID: 22463974 DOI: 10.1016/j.diabet.2012.02.003] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Revised: 02/07/2012] [Accepted: 02/08/2012] [Indexed: 12/16/2022]
Abstract
AIMS Recent genome-wide association studies (GWAS) and previous approaches have identified many genetic variants associated with type 2 diabetes (T2D) in populations of European descent, but their contribution in Arab populations from North Africa is unknown. Our study aimed to validate these markers and to assess their combined effects, using large case-control studies of Moroccan and Tunisian individuals. METHODS Overall, 44 polymorphisms, located at 37 validated European loci, were first analyzed in 1055 normoglycaemic controls and 1193 T2D cases from Morocco. Associations and trends were then assessed in 942 normoglycaemic controls and 1446 T2D cases from Tunisia. Finally, their ability to discriminate cases from controls was evaluated. RESULTS Carrying a genetic variant in BCL11A, ADAMTS9, IGF2BP2, WFS1, CDKAL1, TP53INP1, CDKN2A/B, TCF7L2, KCNQ1, HNF1A, FTO, MC4R and GCK increased the risk of T2D when assessing the Moroccan and Tunisian samples together. Each additional risk allele increased the susceptibility for developing the disease by 12% (P = 9.0 × 10(-9)). Genotype information for 13 polymorphisms slightly improved the classification of North Africans with and without T2D, as assessed by clinical parameters, with an increase in the area under the receiver operating characteristic curve from 0.64 to 0.67 (P = 0.004). CONCLUSION In addition to TCF7L2, 12 additional loci were found to be shared between Europeans and North African Arabs. As for Europeans, the reliability of genetic testing based on these markers to determine the risk for T2D is low. More genome-wide studies, including next-generation sequencing, in North African populations are needed to identify the genetic variants responsible for ethnic disparities in T2D susceptibility.
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Affiliation(s)
- S Cauchi
- CNRS UMR 8199, Genomics and Metabolic Diseases, Lille, France
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Palmer ND, McDonough CW, Hicks PJ, Roh BH, Wing MR, An SS, Hester JM, Cooke JN, Bostrom MA, Rudock ME, Talbert ME, Lewis JP, Ferrara A, Lu L, Ziegler JT, Sale MM, Divers J, Shriner D, Adeyemo A, Rotimi CN, Ng MCY, Langefeld CD, Freedman BI, Bowden DW, Voight BF, Scott LJ, Steinthorsdottir V, Morris AP, Dina C, Welch RP, Zeggini E, Huth C, Aulchenko YS, Thorleifsson G, McCulloch LJ, Ferreira T, Grallert H, Amin N, Wu G, Willer CJ, Raychaudhuri S, McCarroll SA, Langenberg C, Hofmann OM, Dupuis J, Qi L, Segrè AV, van Hoek M, Navarro P, Ardlie K, Balkau B, Benediktsson R, Bennett AJ, Blagieva R, Boerwinkle E, Bonnycastle LL, Boström KB, Bravenboer B, Bumpstead S, Burtt NP, Charpentier G, Chines PS, Cornelis M, Couper DJ, Crawford G, Doney ASF, Elliott KS, Elliott AL, Erdos MR, Fox CS, Franklin CS, Ganser M, Gieger C, Grarup N, Green T, Griffin S, Groves CJ, Guiducci C, Hadjadj S, Hassanali N, Herder C, Isomaa B, Jackson AU, Johnson PRV, Jørgensen T, Kao WHL, Klopp N, Kong A, Kraft P, Kuusisto J, Lauritzen T, Li M, Lieverse A, Lindgren CM, Lyssenko V, Marre M, Meitinger T, Midthjell K, Morken MA, Narisu N, Nilsson P, Owen KR, Payne F, Perry JRB, Petersen AK, Platou C, Proença C, Prokopenko I, Rathmann W, Rayner NW, Robertson NR, Rocheleau G, Roden M, Sampson MJ, Saxena R, Shields BM, Shrader P, Sigurdsson G, Sparsø T, Strassburger K, Stringham HM, Sun Q, Swift AJ, Thorand B, Tichet J, Tuomi T, van Dam RM, van Haeften TW, van Herpt T, van Vliet-Ostaptchouk JV, Walters GB, Weedon MN, Wijmenga C, Witteman J, Bergman RN, Cauchi S, Collins FS, Gloyn AL, Gyllensten U, Hansen T, Hide WA, Hitman GA, Hofman A, Hunter DJ, Hveem K, Laakso M, Mohlke KL, Morris AD, Palmer CNA, Pramstaller PP, Rudan I, Sijbrands E, Stein LD, Tuomilehto J, Uitterlinden A, Walker M, Wareham NJ, Watanabe RM, Abecasis GR, Boehm BO, Campbell H, Daly MJ, Hattersley AT, Hu FB, Meigs JB, Pankow JS, Pedersen O, Wichmann HE, Barroso I, Florez JC, Frayling TM, Groop L, Sladek R, Thorsteinsdottir U, Wilson JF, Illig T, Froguel P, van Duijn CM, Stefansson K, Altshuler D, Boehnke M, McCarthy MI, Soranzo N, Wheeler E, Glazer NL, Bouatia-Naji N, Mägi R, Randall J, Johnson T, Elliott P, Rybin D, Henneman P, Dehghan A, Hottenga JJ, Song K, Goel A, Egan JM, Lajunen T, Doney A, Kanoni S, Cavalcanti-Proença C, Kumari M, Timpson NJ, Zabena C, Ingelsson E, An P, O'Connell J, Luan J, Elliott A, McCarroll SA, Roccasecca RM, Pattou F, Sethupathy P, Ariyurek Y, Barter P, Beilby JP, Ben-Shlomo Y, Bergmann S, Bochud M, Bonnefond A, Borch-Johnsen K, Böttcher Y, Brunner E, Bumpstead SJ, Chen YDI, Chines P, Clarke R, Coin LJM, Cooper MN, Crisponi L, Day INM, de Geus EJC, Delplanque J, Fedson AC, Fischer-Rosinsky A, Forouhi NG, Frants R, Franzosi MG, Galan P, Goodarzi MO, Graessler J, Grundy S, Gwilliam R, Hallmans G, Hammond N, Han X, Hartikainen AL, Hayward C, Heath SC, Hercberg S, Hicks AA, Hillman DR, Hingorani AD, Hui J, Hung J, Jula A, Kaakinen M, Kaprio J, Kesaniemi YA, Kivimaki M, Knight B, Koskinen S, Kovacs P, Kyvik KO, Lathrop GM, Lawlor DA, Le Bacquer O, Lecoeur C, Li Y, Mahley R, Mangino M, Manning AK, Martínez-Larrad MT, McAteer JB, McPherson R, Meisinger C, Melzer D, Meyre D, Mitchell BD, Mukherjee S, Naitza S, Neville MJ, Oostra BA, Orrù M, Pakyz R, Paolisso G, Pattaro C, Pearson D, Peden JF, Pedersen NL, Perola M, Pfeiffer AFH, Pichler I, Polasek O, Posthuma D, Potter SC, Pouta A, Province MA, Psaty BM, Rayner NW, Rice K, Ripatti S, Rivadeneira F, Rolandsson O, Sandbaek A, Sandhu M, Sanna S, Sayer AA, Scheet P, Seedorf U, Sharp SJ, Shields B, Sijbrands EJG, Silveira A, Simpson L, Singleton A, Smith NL, Sovio U, Swift A, Syddall H, Syvänen AC, Tanaka T, Tönjes A, Uitterlinden AG, van Dijk KW, Varma D, Visvikis-Siest S, Vitart V, Vogelzangs N, Waeber G, Wagner PJ, Walley A, Ward KL, Watkins H, Wild SH, Willemsen G, Witteman JCM, Yarnell JWG, Zelenika D, Zethelius B, Zhai G, Zhao JH, Zillikens MC, Borecki IB, Loos RJF, Meneton P, Magnusson PKE, Nathan DM, Williams GH, Silander K, Salomaa V, Smith GD, Bornstein SR, Schwarz P, Spranger J, Karpe F, Shuldiner AR, Cooper C, Dedoussis GV, Serrano-Ríos M, Lind L, Palmer LJ, Franks PW, Ebrahim S, Marmot M, Kao WHL, Pramstaller PP, Wright AF, Stumvoll M, Hamsten A, Buchanan TA, Valle TT, Rotter JI, Siscovick DS, Penninx BWJH, Boomsma DI, Deloukas P, Spector TD, Ferrucci L, Cao A, Scuteri A, Schlessinger D, Uda M, Ruokonen A, Jarvelin MR, Waterworth DM, Vollenweider P, Peltonen L, Mooser V, Sladek R. A genome-wide association search for type 2 diabetes genes in African Americans. PLoS One 2012; 7:e29202. [PMID: 22238593 PMCID: PMC3251563 DOI: 10.1371/journal.pone.0029202] [Citation(s) in RCA: 137] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Accepted: 11/22/2011] [Indexed: 12/16/2022] Open
Abstract
African Americans are disproportionately affected by type 2 diabetes (T2DM) yet few studies have examined T2DM using genome-wide association approaches in this ethnicity. The aim of this study was to identify genes associated with T2DM in the African American population. We performed a Genome Wide Association Study (GWAS) using the Affymetrix 6.0 array in 965 African-American cases with T2DM and end-stage renal disease (T2DM-ESRD) and 1029 population-based controls. The most significant SNPs (n = 550 independent loci) were genotyped in a replication cohort and 122 SNPs (n = 98 independent loci) were further tested through genotyping three additional validation cohorts followed by meta-analysis in all five cohorts totaling 3,132 cases and 3,317 controls. Twelve SNPs had evidence of association in the GWAS (P<0.0071), were directionally consistent in the Replication cohort and were associated with T2DM in subjects without nephropathy (P<0.05). Meta-analysis in all cases and controls revealed a single SNP reaching genome-wide significance (P<2.5×10(-8)). SNP rs7560163 (P = 7.0×10(-9), OR (95% CI) = 0.75 (0.67-0.84)) is located intergenically between RND3 and RBM43. Four additional loci (rs7542900, rs4659485, rs2722769 and rs7107217) were associated with T2DM (P<0.05) and reached more nominal levels of significance (P<2.5×10(-5)) in the overall analysis and may represent novel loci that contribute to T2DM. We have identified novel T2DM-susceptibility variants in the African-American population. Notably, T2DM risk was associated with the major allele and implies an interesting genetic architecture in this population. These results suggest that multiple loci underlie T2DM susceptibility in the African-American population and that these loci are distinct from those identified in other ethnic populations.
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Affiliation(s)
- Nicholette D Palmer
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, North Carolina, United States of America.
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Voight BF, Scott LJ, Steinthorsdottir V, Morris AP, Dina C, Welch RP, Zeggini E, Huth C, Aulchenko YS, Thorleifsson G, McCulloch LJ, Ferreira T, Grallert H, Amin N, Wu G, Willer CJ, Raychaudhuri S, McCarroll SA, Langenberg C, Hofmann OM, Dupuis J, Qi L, Segrè AV, van Hoek M, Navarro P, Ardlie K, Balkau B, Benediktsson R, Bennett AJ, Blagieva R, Boerwinkle E, Bonnycastle LL, Boström KB, Bravenboer B, Bumpstead S, Burtt NP, Charpentier G, Chines PS, Cornelis M, Couper DJ, Crawford G, Doney ASF, Elliott KS, Elliott AL, Erdos MR, Fox CS, Franklin CS, Ganser M, Gieger C, Grarup N, Green T, Griffin S, Groves CJ, Guiducci C, Hadjadj S, Hassanali N, Herder C, Isomaa B, Jackson AU, Johnson PRV, Jørgensen T, Kao WHL, Klopp N, Kong A, Kraft P, Kuusisto J, Lauritzen T, Li M, Lieverse A, Lindgren CM, Lyssenko V, Marre M, Meitinger T, Midthjell K, Morken MA, Narisu N, Nilsson P, Owen KR, Payne F, Perry JRB, Petersen AK, Platou C, Proença C, Prokopenko I, Rathmann W, Rayner NW, Robertson NR, Rocheleau G, Roden M, Sampson MJ, Saxena R, Shields BM, Shrader P, Sigurdsson G, Sparsø T, Strassburger K, Stringham HM, Sun Q, Swift AJ, Thorand B, Tichet J, Tuomi T, van Dam RM, van Haeften TW, van Herpt T, van Vliet-Ostaptchouk JV, Walters GB, Weedon MN, Wijmenga C, Witteman J, Bergman RN, Cauchi S, Collins FS, Gloyn AL, Gyllensten U, Hansen T, Hide WA, Hitman GA, Hofman A, Hunter DJ, Hveem K, Laakso M, Mohlke KL, Morris AD, Palmer CNA, Pramstaller PP, Rudan I, Sijbrands E, Stein LD, Tuomilehto J, Uitterlinden A, Walker M, Wareham NJ, Watanabe RM, Abecasis GR, Boehm BO, Campbell H, Daly MJ, Hattersley AT, Hu FB, Meigs JB, Pankow JS, Pedersen O, Wichmann HE, Barroso I, Florez JC, Frayling TM, Groop L, Sladek R, Thorsteinsdottir U, Wilson JF, Illig T, Froguel P, van Duijn CM, Stefansson K, Altshuler D, Boehnke M, McCarthy MI. Erratum: Corrigendum: Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis. Nat Genet 2011. [DOI: 10.1038/ng0411-388b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Yamauchi T, Hara K, Maeda S, Yasuda K, Takahashi A, Horikoshi M, Nakamura M, Fujita H, Grarup N, Cauchi S, Ng DPK, Ma RCW, Tsunoda T, Kubo M, Watada H, Maegawa H, Okada-Iwabu M, Iwabu M, Shojima N, Shin HD, Andersen G, Witte DR, Jørgensen T, Lauritzen T, Sandbæk A, Hansen T, Ohshige T, Omori S, Saito I, Kaku K, Hirose H, So WY, Beury D, Chan JCN, Park KS, Tai ES, Ito C, Tanaka Y, Kashiwagi A, Kawamori R, Kasuga M, Froguel P, Pedersen O, Kamatani N, Nakamura Y, Kadowaki T. A genome-wide association study in the Japanese population identifies susceptibility loci for type 2 diabetes at UBE2E2 and C2CD4A-C2CD4B. Nat Genet 2010; 42:864-8. [PMID: 20818381 DOI: 10.1038/ng.660] [Citation(s) in RCA: 203] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2010] [Accepted: 08/11/2010] [Indexed: 12/19/2022]
Abstract
We conducted a genome-wide association study of type 2 diabetes (T2D) using 459,359 SNPs in a Japanese population with a three-stage study design (stage 1, 4,470 cases and 3,071 controls; stage 2, 2,886 cases and 3,087 controls; stage 3, 3,622 cases and 2,356 controls). We identified new associations in UBE2E2 on chromosome 3 and in C2CD4A-C2CD4B on chromosome 15 at genome-wide significant levels (rs7612463 in UBE2E2, combined P = 2.27 × 10⁻⁹; rs7172432 in C2CD4A-C2CD4B, combined P = 3.66 × 10⁻⁹). The association of these two loci with T2D was replicated in other east Asian populations. In the European populations, the C2CD4A-C2CD4B locus was significantly associated with T2D, and a combined analysis of all populations gave P = 8.78 × 10⁻¹⁴, whereas the UBE2E2 locus did not show association to T2D. In conclusion, we identified two new loci at UBE2E2 and C2CD4A-C2CD4B associated with susceptibility to T2D.
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Affiliation(s)
- Toshimasa Yamauchi
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
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Voight BF, Scott LJ, Steinthorsdottir V, Morris AP, Dina C, Welch RP, Zeggini E, Huth C, Aulchenko YS, Thorleifsson G, McCulloch LJ, Ferreira T, Grallert H, Amin N, Wu G, Willer CJ, Raychaudhuri S, McCarroll SA, Langenberg C, Hofmann OM, Dupuis J, Qi L, Segrè AV, van Hoek M, Navarro P, Ardlie K, Balkau B, Benediktsson R, Bennett AJ, Blagieva R, Boerwinkle E, Bonnycastle LL, Bengtsson Boström K, Bravenboer B, Bumpstead S, Burtt NP, Charpentier G, Chines PS, Cornelis M, Couper DJ, Crawford G, Doney ASF, Elliott KS, Elliott AL, Erdos MR, Fox CS, Franklin CS, Ganser M, Gieger C, Grarup N, Green T, Griffin S, Groves CJ, Guiducci C, Hadjadj S, Hassanali N, Herder C, Isomaa B, Jackson AU, Johnson PRV, Jørgensen T, Kao WHL, Klopp N, Kong A, Kraft P, Kuusisto J, Lauritzen T, Li M, Lieverse A, Lindgren CM, Lyssenko V, Marre M, Meitinger T, Midthjell K, Morken MA, Narisu N, Nilsson P, Owen KR, Payne F, Perry JRB, Petersen AK, Platou C, Proença C, Prokopenko I, Rathmann W, Rayner NW, Robertson NR, Rocheleau G, Roden M, Sampson MJ, Saxena R, Shields BM, Shrader P, Sigurdsson G, Sparsø T, Strassburger K, Stringham HM, Sun Q, Swift AJ, Thorand B, Tichet J, Tuomi T, van Dam RM, van Haeften TW, van Herpt T, van Vliet-Ostaptchouk JV, Walters GB, Weedon MN, Wijmenga C, Witteman J, Bergman RN, Cauchi S, Collins FS, Gloyn AL, Gyllensten U, Hansen T, Hide WA, Hitman GA, Hofman A, Hunter DJ, Hveem K, Laakso M, Mohlke KL, Morris AD, Palmer CNA, Pramstaller PP, Rudan I, Sijbrands E, Stein LD, Tuomilehto J, Uitterlinden A, Walker M, Wareham NJ, Watanabe RM, Abecasis GR, Boehm BO, Campbell H, Daly MJ, Hattersley AT, Hu FB, Meigs JB, Pankow JS, Pedersen O, Wichmann HE, Barroso I, Florez JC, Frayling TM, Groop L, Sladek R, Thorsteinsdottir U, Wilson JF, Illig T, Froguel P, van Duijn CM, Stefansson K, Altshuler D, Boehnke M, McCarthy MI. Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis. Nat Genet 2010; 42:579-89. [PMID: 20581827 DOI: 10.1038/ng.609] [Citation(s) in RCA: 1338] [Impact Index Per Article: 95.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2010] [Accepted: 05/26/2010] [Indexed: 12/11/2022]
Abstract
By combining genome-wide association data from 8,130 individuals with type 2 diabetes (T2D) and 38,987 controls of European descent and following up previously unidentified meta-analysis signals in a further 34,412 cases and 59,925 controls, we identified 12 new T2D association signals with combined P<5x10(-8). These include a second independent signal at the KCNQ1 locus; the first report, to our knowledge, of an X-chromosomal association (near DUSP9); and a further instance of overlap between loci implicated in monogenic and multifactorial forms of diabetes (at HNF1A). The identified loci affect both beta-cell function and insulin action, and, overall, T2D association signals show evidence of enrichment for genes involved in cell cycle regulation. We also show that a high proportion of T2D susceptibility loci harbor independent association signals influencing apparently unrelated complex traits.
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Affiliation(s)
- Benjamin F Voight
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
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Grau K, Cauchi S, Holst C, Astrup A, Martinez JA, Saris WHM, Blaak EE, Oppert JM, Arner P, Rössner S, Macdonald IA, Klimcakova E, Langin D, Pedersen O, Froguel P, Sørensen TIA. TCF7L2 rs7903146-macronutrient interaction in obese individuals' responses to a 10-wk randomized hypoenergetic diet. Am J Clin Nutr 2010; 91:472-9. [PMID: 20032493 DOI: 10.3945/ajcn.2009.27947] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Transcription factor 7-like 2 (TCF7L2) rs7903146 associates with type 2 diabetes and may operate via impaired glucagon-like peptide 1 secretion, which is stimulated more by fat than by carbohydrate ingestion. OBJECTIVE The objective was to examine the interaction between TCF7L2 rs7903146 and dietary fat and carbohydrate [high-fat, low-carbohydrate: 40-45% of energy as fat (HF); compared with low-fat, high-carbohydrate: 20-25% of energy as fat (LF)] in obese individuals' responses to a 10-wk hypoenergetic diet (-600 kcal/d). DESIGN European, obese participants (n = 771) were randomly assigned to receive an HF or an LF diet. Body weight, fat mass (FM), fat-free mass (FFM), waist circumference (WC), resting energy expenditure (REE), fasting fat oxidation in percentage of REE (FatOx), homeostasis model assessed insulin release (HOMA-beta), and HOMA-insulin resistance (HOMA-IR) were determined at baseline and after the intervention; 739 individuals were genotyped for rs7903146. RESULTS Average weight loss was 6.9 kg with the LF and 6.6 kg with the HF (difference between diets, NS) diet. Among individuals who were homozygous for the T-risk allele, those in the HF diet group experienced smaller weight losses (Deltaweight) (2.6 kg; P = 0.009; n = 622), smaller DeltaFFM (1.6 kg; P = 0.027; n = 609), smaller DeltaWC (3.3 cm; P = 0.010; n = 608), and a smaller DeltaHOMA-IR (1.3 units; P = 0.004; n = 615) than did the LF diet group. For C allele carriers, there were no differences between the HF and LF diet groups. For the HF diet group, each additional T allele was associated with a reduced loss of FM (0.67 kg; P = 0.019; n = 609). TCF7L2 rs7903146 was not associated with DeltaREE, DeltaFatOx, DeltaHOMA-beta, or dropout. CONCLUSION Our results suggest that obese individuals who are homozygous for the TCF7L2 rs7903146 T-risk allele are more sensitive to LF than to HF weight-loss diets.
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Affiliation(s)
- Katrine Grau
- Institute of Preventive Medicine Copenhagen University Hospital, Centre for Health and Society, Copenhagen, Denmark.
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Balkau B, Lange C, Fezeu L, Tichet J, de Lauzon-Guillain B, Czernichow S, Fumeron F, Froguel P, Vaxillaire M, Cauchi S, Ducimetière P, Eschwège E. Predicting diabetes: clinical, biological, and genetic approaches: data from the Epidemiological Study on the Insulin Resistance Syndrome (DESIR). Diabetes Care 2008; 31:2056-61. [PMID: 18689695 PMCID: PMC2551654 DOI: 10.2337/dc08-0368] [Citation(s) in RCA: 183] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
OBJECTIVE To provide a simple clinical diabetes risk score and to identify characteristics that predict later diabetes using variables available in the clinic setting as well as biological variables and polymorphisms. RESEARCH DESIGN AND METHODS Incident diabetes was studied in 1,863 men and 1,954 women, 30-65 years of age at baseline, with diabetes defined by treatment or by fasting plasma glucose >or=7.0 mmol/l at 3-yearly examinations over 9 years. Sex-specific logistic regression equations were used to select variables for prediction. RESULTS A total of 140 men and 63 women developed diabetes. The predictive clinical variables were waist circumference and hypertension in both sexes, smoking in men, and diabetes in the family in women. Discrimination, as measured by the area under the receiver operating curves (AROCs), were 0.713 for men and 0.827 for women, a little higher than for the Finish Diabetes Risk (FINDRISC) score, with fewer variables in the score. Combining clinical and biological variables, the predictive equation included fasting glucose, waist circumference, smoking, and gamma-glutamyltransferase for men and fasting glucose, BMI, triglycerides, and diabetes in family for women. The number of TCF7L2 and IL6 deleterious alleles was predictive in both sexes, but after including the above clinical and biological variables, this variable was only predictive in women (P < 0.03) and the AROC statistics increased only marginally. CONCLUSIONS The best clinical predictor of diabetes is adiposity, and baseline glucose is the best biological predictor. Clinical and biological predictors differed marginally between men and women. The genetic polymorphisms added little to the prediction of diabetes.
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Affiliation(s)
- Beverley Balkau
- INSERM U780-IFR69, Villejuif, France/University Paris-Sud, Orsay, France.
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Cauchi S, Vaxillaire M, Choquet H, Durand E, Duval A, Polak M, Froguel P. No major contribution of TCF7L2 sequence variants to maturity onset of diabetes of the young (MODY) or neonatal diabetes mellitus in French white subjects. Diabetologia 2007; 50:214-6. [PMID: 17093940 DOI: 10.1007/s00125-006-0505-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2006] [Accepted: 10/02/2006] [Indexed: 11/25/2022]
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Abstract
Phase II detoxification of carcinogens is reported to mediate some of the anticarcinogenesis effects of candidate chemopreventive agents. We explored the interaction between sequence variation in the GSTP1 gene promoter and candidate chemopreventive exposure in regulating human GSTP1 expression. Polymorphisms along 1.8 kb of the GSTP1 promoter were identified in leukocytes [peripheral blood mononuclear cells (PBMC)] from 40 Caucasian subjects. Ten promoter polymorphisms (9 previously unreported) displayed strong linkage disequilibrium, yielding identification of three frequently observed haplotypes [HAP1 (43%), HAP2 (36%), and HAP3 (8%)]. Each haplotype was cloned into luciferase reporter constructs and transfected into normal human bronchial epithelial cells. Basal HAP3 reporter activity was significantly elevated (1.8-fold) but decreased to the same levels as HAP2 and HAP1 with increasing concentrations of sulforaphane, benzyl isothiocyanate (BITC), and epigallocatechin gallate (EGCG). To confirm native HAP3 functionality, we quantitated mRNA expression in uncultured PBMCs and in laser microdissected normal lung epithelial cells (MNLEC) from the same patients. Basal mRNA expression was higher in HAP3 individuals [1.8-fold (PBMC) and 4-fold (MNLEC) for HAP3 heterozygotes and 2.3-fold (PBMC), and 15-fold (MNLEC) for the HAP3 homozygote] than in the other genotypes. PBMC GSTP1 mRNA expression correlated to MNLEC expression (R2 = 0.77). After culture and in vitro exposure to sulforaphane, BITC, or EGCG, the elevated GSTP1 mRNA expression of PBMCs from HAP3 individuals decreased to common expression levels. Elevated HAP3 function was confirmed at the protein level in PBMCs (5-fold higher for HAP3 heterozygotes and 7.6-fold for the HAP3 homozygote). These data suggest a potentially protective GSTP1 promoter haplotype and unpredicted inhibitory chemopreventive agent-haplotype interactions.
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Affiliation(s)
- Stephane Cauchi
- Laboratory of Human Toxicology and Molecular Epidemiology, Wadsworth Center, New York State Department of Health, NY, USA
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Han W, Cauchi S, Herman JG, Spivack SD. DNA methylation mapping by tag-modified bisulfite genomic sequencing. Anal Biochem 2006; 355:50-61. [PMID: 16797472 DOI: 10.1016/j.ab.2006.05.010] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [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: 01/26/2006] [Revised: 04/13/2006] [Accepted: 05/09/2006] [Indexed: 11/25/2022]
Abstract
A tag-modified bisulfite genomic sequencing (tBGS) method employing direct cycle sequencing of polymerase chain reaction (PCR) products at kilobase scale, without conventional DNA fragment cloning, was developed for simplified evaluation of DNA methylation sites. The method entails subjecting bisulfite-modified genomic DNA to a second-round PCR amplification employing GC-tagged primers. Qualitative results from tBGS closely correlated with those from conventional BGS (R=0.935, p=0.002). In application, the intertissue and interindividual CpG methylation differences in promoter sequence for two genes, CYP1B1 and GSTP1, were then explored across four human tissue types (peripheral blood cells, exfoliated buccal cells, paired nontumor-tumor lung tissues), and two lung cell types in culture (normal NHBE and malignant A549). Predominantly conserved methylation maps for the two gene promoters were apparent across donors and tissues. At any given CpG site, variation in the degree of methylation could be determined by the relative height of C and T peaks in the sequencing trace. Methylation maps for the GSTP1 promoter diverged between NHBE (unmethylated) and A549 (completely methylated) cells in a previously unexplored upstream region, correlating with a 2.7-fold difference in GSTP1 mRNA expression (p<0.01). The tBGS method simplifies detailed methylation scanning of kilobase-scale genomic DNA, facilitating more ambitious genomic methylation mapping studies.
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Affiliation(s)
- Weiguo Han
- Laboratory of Human Toxicology and Molecular Epidemiology, Wadsworth Center, NYS Department of Health, Albany, NY 12201, USA
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Hoogland S, Sukhovatkin V, Howard I, Cauchi S, Levina L, Sargent EH. A solution-processed 1.53 mum quantum dot laser with temperature-invariant emission wavelength. Opt Express 2006; 14:3273-3281. [PMID: 19516469 DOI: 10.1364/oe.14.003273] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Sources of coherent, monochromatic short-wavelength infrared (1-2 mum) light are essential in telecommunications, biomedical diagnosis, and optical sensing. Today's semiconductor lasers are made by epitaxial growth on a lattice-matched single-crystal substrate. This strategy is incompatible with integration on silicon. Colloidal quantum dots grown in solution can, in contrast, be coated onto any surface. Here we show a 1.53 mum laser fabricated using a remarkably simple process: dipping a glass capillary into a colloidal suspension of semiconductor quantum dots. We developed the procedures to produce a smooth, low-scattering-loss film inside the capillary, resulting in a whispering gallery mode laser with a well-defined threshold. While there exist three prior reports of optical gain in infrared-emitting colloidal quantum dots [1,2,3], this work represents the first report of an infrared laser made using solution processing. We also report dlambda(max)/dT, the temperature-sensitivity of lasing wavelength, of 0.03 nm/K, the lowest ever reported in a colloidal quantum dot system and 10 times lower than in traditional semiconductor quantum wells.
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Sukhovatkin V, Musikhin S, Gorelikov I, Cauchi S, Bakueva L, Kumacheva E, Sargent EH. Room-temperature amplified spontaneous emission at 1300 nm in solution-processed PbS quantum-dot films. Opt Lett 2005; 30:171-173. [PMID: 15675703 DOI: 10.1364/ol.30.000171] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
We report room-temperature amplified spontaneous emission and spectral narrowing at infrared wavelengths in solution-processed films made up of PbS quantum-dot nanocrystals. The results are relevant to optical amplification and lasing integrated upon a variety of substrates. The active optical medium operates at room temperature without any additional matrix material, providing an optical gain of 260 cm(-1) and a pump threshold of 1 mJ/cm(-2). Nanocrystals synthesized in an aqueous solution and stabilized by use of short ligands result in high quantum-dot volume fractions in solid films and in a redshift emission relative to absorption.
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Affiliation(s)
- V Sukhovatkin
- Department of Electrical and Computer Engineering, University of Toronto, Toronto M5S 1A4, Canada
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Cauchi S, Stücker I, Solas C, Laurent-Puig P, Cénée S, Hémon D, Jacquet M, Kremers P, Beaune P, Massaad-Massade L. Polymorphisms of human aryl hydrocarbon receptor (AhR) gene in a French population: relationship with CYP1A1 inducibility and lung cancer. Carcinogenesis 2001; 22:1819-24. [PMID: 11698344 DOI: 10.1093/carcin/22.11.1819] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The Ah receptor (AhR) is a ligand-dependent transcription factor that positively regulates the expression of the CYP1A1 gene. We investigated the genetic polymorphisms of the AhR gene including the promoter, and examined the link between these polymorphisms, CYP1A1 inducibility and the lung cancer incidence. The AhR promoter region and the 11 exons of 30 subjects were screened. Among the three polymorphisms found, two [(2417)(A/G) ((157)G/A)] have never been described previously. The (1721)(G/A) and (2417)(A/G) are localized in exon 10 and lead to Arg(554)Lys and Met(786)Val substitutions, respectively. The other polymorphism was found in the 5'-untranslated region, resulting in the substitution of a G by an A at position 157 (157)(G/A). To evaluate the frequency of this allelic variant found, a DNA library of a case-control study of lung cancer (162 controls and 177 patients) was studied. There is no significant association between (1721)(G/A), (157)(G/A) and lung cancer: (1721)(G/A) and (157)(G/A) were detected at the same allele frequency of 0.086 and 0.25, respectively in both controls and patients. (2417)(A/G) was found in only one control of 100 (allele frequency 0.005). Statistical analysis did not show any relationship between both (1721)(G/A) and (157)(G/A) polymorphisms found and CYP1A1 inducibility. Considering the rareness of the (2417)(A/G) allelic variant we were not able to evaluate its association with inducibility. In conclusion, none of the polymorphisms were found to play a key role in the CYP1A1 inducibility or in the susceptibility to develop lung cancer.
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Affiliation(s)
- S Cauchi
- Laboratoire de Toxicologie Moléculaire, U-490 INSERM, 45 rue des Saints-Pères, F-75270 Paris Cedex, France
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