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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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