101
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Spracklen CN, Shi J, Vadlamudi S, Wu Y, Zou M, Raulerson CK, Davis JP, Zeynalzadeh M, Jackson K, Yuan W, Wang H, Shou W, Wang Y, Luo J, Lange LA, Lange EM, Popkin BM, Gordon-Larsen P, Du S, Huang W, Mohlke KL. Identification and functional analysis of glycemic trait loci in the China Health and Nutrition Survey. PLoS Genet 2018; 14:e1007275. [PMID: 29621232 PMCID: PMC5886383 DOI: 10.1371/journal.pgen.1007275] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 02/23/2018] [Indexed: 12/17/2022] Open
Abstract
To identify genetic contributions to type 2 diabetes (T2D) and related glycemic traits (fasting glucose, fasting insulin, and HbA1c), we conducted genome-wide association analyses (GWAS) in up to 7,178 Chinese subjects from nine provinces in the China Health and Nutrition Survey (CHNS). We examined patterns of population structure within CHNS and found that allele frequencies differed across provinces, consistent with genetic drift and population substructure. We further validated 32 previously described T2D- and glycemic trait-loci, including G6PC2 and SIX3-SIX2 associated with fasting glucose. At G6PC2, we replicated a known fasting glucose-associated variant (rs34177044) and identified a second signal (rs2232326), a low-frequency (4%), probably damaging missense variant (S324P). A variant within the lead fasting glucose-associated signal at SIX3-SIX2 co-localized with pancreatic islet expression quantitative trait loci (eQTL) for SIX3, SIX2, and three noncoding transcripts. To identify variants functionally responsible for the fasting glucose association at SIX3-SIX2, we tested five candidate variants for allelic differences in regulatory function. The rs12712928-C allele, associated with higher fasting glucose and lower transcript expression level, showed lower transcriptional activity in reporter assays and increased binding to GABP compared to the rs12712928-G, suggesting that rs12712928-C contributes to elevated fasting glucose levels by disrupting an islet enhancer, resulting in reduced gene expression. Taken together, these analyses identified multiple loci associated with glycemic traits across China, and suggest a regulatory mechanism at the SIX3-SIX2 fasting glucose GWAS locus.
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Affiliation(s)
- Cassandra N. Spracklen
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Jinxiu Shi
- Department of Genetics, Shanghai-MOST Key Laboratory of Heath and Disease Genomics, Chinese National Human Genome Center and Shanghai Industrial Technology Institute, Shanghai, China
| | - Swarooparani Vadlamudi
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Ying Wu
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Meng Zou
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Chelsea K. Raulerson
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - James P. Davis
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Monica Zeynalzadeh
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Kayla Jackson
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Wentao Yuan
- Department of Genetics, Shanghai-MOST Key Laboratory of Heath and Disease Genomics, Chinese National Human Genome Center and Shanghai Industrial Technology Institute, Shanghai, China
| | - Haifeng Wang
- Department of Genetics, Shanghai-MOST Key Laboratory of Heath and Disease Genomics, Chinese National Human Genome Center and Shanghai Industrial Technology Institute, Shanghai, China
| | - Weihua Shou
- Department of Genetics, Shanghai-MOST Key Laboratory of Heath and Disease Genomics, Chinese National Human Genome Center and Shanghai Industrial Technology Institute, Shanghai, China
| | - Ying Wang
- Department of Genetics, Shanghai-MOST Key Laboratory of Heath and Disease Genomics, Chinese National Human Genome Center and Shanghai Industrial Technology Institute, Shanghai, China
| | - Jingchun Luo
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Leslie A. Lange
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Ethan M. Lange
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Barry M. Popkin
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Penny Gordon-Larsen
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Shufa Du
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Wei Huang
- Department of Genetics, Shanghai-MOST Key Laboratory of Heath and Disease Genomics, Chinese National Human Genome Center and Shanghai Industrial Technology Institute, Shanghai, China
| | - Karen L. Mohlke
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- * E-mail:
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102
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Small KS, Todorčević M, Civelek M, El-Sayed Moustafa JS, Wang X, Simon MM, Fernandez-Tajes J, Mahajan A, Horikoshi M, Hugill A, Glastonbury CA, Quaye L, Neville MJ, Sethi S, Yon M, Pan C, Che N, Viñuela A, Tsai PC, Nag A, Buil A, Thorleifsson G, Raghavan A, Ding Q, Morris AP, Bell JT, Thorsteinsdottir U, Stefansson K, Laakso M, Dahlman I, Arner P, Gloyn AL, Musunuru K, Lusis AJ, Cox RD, Karpe F, McCarthy MI. Regulatory variants at KLF14 influence type 2 diabetes risk via a female-specific effect on adipocyte size and body composition. Nat Genet 2018; 50:572-580. [PMID: 29632379 PMCID: PMC5935235 DOI: 10.1038/s41588-018-0088-x] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 02/15/2018] [Indexed: 12/30/2022]
Abstract
Individual risk of type 2 diabetes (T2D) is modified by perturbations to the mass, distribution and function of adipose tissue. To investigate the mechanisms underlying these associations, we explored the molecular, cellular and whole-body effects of T2D-associated alleles near KLF14. We show that KLF14 diabetes-risk alleles act in adipose tissue to reduce KLF14 expression and modulate, in trans, the expression of 385 genes. We demonstrate, in human cellular studies, that reduced KLF14 expression increases pre-adipocyte proliferation but disrupts lipogenesis, and in mice, that adipose tissue-specific deletion of Klf14 partially recapitulates the human phenotype of insulin resistance, dyslipidemia and T2D. We show that carriers of the KLF14 T2D risk allele shift body fat from gynoid stores to abdominal stores and display a marked increase in adipocyte cell size, and that these effects on fat distribution, and the T2D association, are female specific. The metabolic risk associated with variation at this imprinted locus depends on the sex both of the subject and of the parent from whom the risk allele derives.
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Affiliation(s)
- Kerrin S Small
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK.
| | - Marijana Todorčević
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, UK
| | - Mete Civelek
- Center for Public Health Genomics, Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
- Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | | | - Xiao Wang
- Cardiovascular Institute, Department of Medicine, Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Michelle M Simon
- Biocomputing, Medical Research Council Harwell Institute, Oxford, UK
| | | | - Anubha Mahajan
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Momoko Horikoshi
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Alison Hugill
- Genetics of Type 2 Diabetes, Medical Research Council Harwell Institute, Oxford, UK
| | - Craig A Glastonbury
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Lydia Quaye
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Matt J Neville
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, UK
- Oxford NIHR Biomedical Research Centre, Churchill Hospital, Oxford, UK
| | - Siddharth Sethi
- Biocomputing, Medical Research Council Harwell Institute, Oxford, UK
| | - Marianne Yon
- Genetics of Type 2 Diabetes, Medical Research Council Harwell Institute, Oxford, UK
| | - Calvin Pan
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Nam Che
- Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ana Viñuela
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Pei-Chien Tsai
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Abhishek Nag
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Alfonso Buil
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | | | | | - Qiurong Ding
- CAS Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, PR China
| | - Andrew P Morris
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Department of Biostatistics, University of Liverpool, Liverpool, UK
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Unnur Thorsteinsdottir
- deCODE Genetics, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Kari Stefansson
- deCODE Genetics, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Markku Laakso
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Ingrid Dahlman
- Department of Medicine, Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Peter Arner
- Department of Medicine, Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Anna L Gloyn
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford NIHR Biomedical Research Centre, Churchill Hospital, Oxford, UK
| | - Kiran Musunuru
- Cardiovascular Institute, Department of Medicine, Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Aldons J Lusis
- Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Roger D Cox
- Genetics of Type 2 Diabetes, Medical Research Council Harwell Institute, Oxford, UK
| | - Fredrik Karpe
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, UK
- Oxford NIHR Biomedical Research Centre, Churchill Hospital, Oxford, UK
| | - Mark I McCarthy
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, UK.
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
- Oxford NIHR Biomedical Research Centre, Churchill Hospital, Oxford, UK.
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103
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Schugar RC, Shih DM, Warrier M, Helsley RN, Burrows A, Ferguson D, Brown AL, Gromovsky AD, Heine M, Chatterjee A, Li L, Li XS, Wang Z, Willard B, Meng Y, Kim H, Che N, Pan C, Lee RG, Crooke RM, Graham MJ, Morton RE, Langefeld CD, Das SK, Rudel LL, Zein N, McCullough AJ, Dasarathy S, Tang WHW, Erokwu BO, Flask CA, Laakso M, Civelek M, Naga Prasad SV, Heeren J, Lusis AJ, Hazen SL, Brown JM. The TMAO-Producing Enzyme Flavin-Containing Monooxygenase 3 Regulates Obesity and the Beiging of White Adipose Tissue. Cell Rep 2018. [PMID: 28636934 DOI: 10.1016/j.celrep.2017.05.077] [Citation(s) in RCA: 163] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Emerging evidence suggests that microbes resident in the human intestine represent a key environmental factor contributing to obesity-associated disorders. Here, we demonstrate that the gut microbiota-initiated trimethylamine N-oxide (TMAO)-generating pathway is linked to obesity and energy metabolism. In multiple clinical cohorts, systemic levels of TMAO were observed to strongly associate with type 2 diabetes. In addition, circulating TMAO levels were associated with obesity traits in the different inbred strains represented in the Hybrid Mouse Diversity Panel. Further, antisense oligonucleotide-mediated knockdown or genetic deletion of the TMAO-producing enzyme flavin-containing monooxygenase 3 (FMO3) conferred protection against obesity in mice. Complimentary mouse and human studies indicate a negative regulatory role for FMO3 in the beiging of white adipose tissue. Collectively, our studies reveal a link between the TMAO-producing enzyme FMO3 and obesity and the beiging of white adipose tissue.
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Affiliation(s)
- Rebecca C Schugar
- Department of Cellular and Molecular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA; Center for Microbiome and Human Health, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Diana M Shih
- Departments of Medicine, Microbiology, and Human Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Manya Warrier
- Department of Cellular and Molecular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA; Center for Microbiome and Human Health, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Robert N Helsley
- Department of Cellular and Molecular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA; Center for Microbiome and Human Health, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Amy Burrows
- Department of Cellular and Molecular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA; Center for Microbiome and Human Health, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Daniel Ferguson
- Department of Cellular and Molecular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA; Center for Microbiome and Human Health, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Amanda L Brown
- Department of Cellular and Molecular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA; Center for Microbiome and Human Health, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Anthony D Gromovsky
- Department of Cellular and Molecular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA; Center for Microbiome and Human Health, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Markus Heine
- Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | | | - Lin Li
- Department of Cellular and Molecular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA; Center for Microbiome and Human Health, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Xinmin S Li
- Department of Cellular and Molecular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA; Center for Microbiome and Human Health, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Zeneng Wang
- Department of Cellular and Molecular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA; Center for Microbiome and Human Health, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Belinda Willard
- Department of Cellular and Molecular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA; Center for Microbiome and Human Health, Cleveland Clinic, Cleveland, OH 44195, USA
| | - YongHong Meng
- Departments of Medicine, Microbiology, and Human Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Hanjun Kim
- Departments of Medicine, Microbiology, and Human Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Nam Che
- Departments of Medicine, Microbiology, and Human Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Calvin Pan
- Departments of Medicine, Microbiology, and Human Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Richard G Lee
- Cardiovascular Group, Antisense Drug Discovery, Ionis Pharmaceuticals, Inc., Carlsbad, CA 92010, USA
| | - Rosanne M Crooke
- Cardiovascular Group, Antisense Drug Discovery, Ionis Pharmaceuticals, Inc., Carlsbad, CA 92010, USA
| | - Mark J Graham
- Cardiovascular Group, Antisense Drug Discovery, Ionis Pharmaceuticals, Inc., Carlsbad, CA 92010, USA
| | - Richard E Morton
- Department of Cellular and Molecular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Carl D Langefeld
- Department of Biostatistical Sciences, Wake Forest University School of Medicine, Winston-Salem, NC 27157-1040, USA
| | - Swapan K Das
- Department of Endocrinology and Metabolism, Wake Forest University School of Medicine, Winston-Salem, NC 27157-1040, USA
| | - Lawrence L Rudel
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest University School of Medicine, Winston-Salem, NC 27157-1040, USA
| | - Nizar Zein
- Department of Gastroenterology and Hepatology, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Arthur J McCullough
- Department of Gastroenterology and Hepatology, Cleveland Clinic, Cleveland, OH 44195, USA
| | | | - W H Wilson Tang
- Department of Cellular and Molecular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA; Center for Microbiome and Human Health, Cleveland Clinic, Cleveland, OH 44195, USA; Department of Cardiovascular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Bernadette O Erokwu
- Departments of Radiology, Biomedical Engineering, and Pediatrics, Case Western Reserve University, Cleveland, OH 44195, USA
| | - Chris A Flask
- Departments of Radiology, Biomedical Engineering, and Pediatrics, Case Western Reserve University, Cleveland, OH 44195, USA
| | - Markku Laakso
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland and Kuopio University Hospital, 70210 Kuopio, Finland
| | - Mete Civelek
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22904, USA
| | | | - Joerg Heeren
- Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Aldons J Lusis
- Departments of Medicine, Microbiology, and Human Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Stanley L Hazen
- Department of Cellular and Molecular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA; Center for Microbiome and Human Health, Cleveland Clinic, Cleveland, OH 44195, USA; Department of Cardiovascular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA
| | - J Mark Brown
- Department of Cellular and Molecular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA; Center for Microbiome and Human Health, Cleveland Clinic, Cleveland, OH 44195, USA.
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104
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Langefeld CD, Comeau ME, Sharma NK, Bowden DW, Freedman BI, Das SK. Transcriptional Regulatory Mechanisms in Adipose and Muscle Tissue Associated with Composite Glucometabolic Phenotypes. Obesity (Silver Spring) 2018; 26:559-569. [PMID: 29377571 PMCID: PMC5821540 DOI: 10.1002/oby.22113] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 10/27/2017] [Accepted: 12/08/2017] [Indexed: 12/13/2022]
Abstract
OBJECTIVE Tissue-specific gene expression is associated with individual metabolic measures. However, these measures may not reflect the true but latent underlying biological phenotype. This study reports gene expression associations with multidimensional glucometabolic characterizations of obesity, glucose homeostasis, and lipid traits. METHODS Factor analysis was computed by using orthogonal rotation to construct composite phenotypes (CPs) from 23 traits in 256 African Americans without diabetes. Genome-wide transcript expression data from adipose and muscle were tested for association with CPs, and expression quantitative trait loci (eQTLs) were identified by associations between cis-acting single-nucleotide polymorphisms (SNPs) and gene expression. RESULTS The factor analysis identified six CPs. CPs 1 through 6 individually explained 34%, 12%, 9%, 8%, 6%, and 5% of the variation in 23 glucometabolic traits studied. There were 3,994 and 929 CP-associated transcripts identified in adipose and muscle tissue, respectively; CP2 had the largest number of associated transcripts. Pathway analysis identified multiple canonical pathways from the CP-associated transcripts. In adipose and muscle, significant cis-eQTLs were identified for 558 and 164 CP-associated transcripts (q-value < 0.01), respectively. CONCLUSIONS Adipose and muscle transcripts comprehensively define pathways involved in regulating glucometabolic disorders. Cis-eQTLs for CP-associated genes may act as primary causal determinants of glucometabolic phenotypes by regulating transcription of key genes.
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Affiliation(s)
- Carl D. Langefeld
- Department of Biostatistical Sciences, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC 27157
| | - Mary E. Comeau
- Department of Biostatistical Sciences, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC 27157
| | - Neeraj K. Sharma
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157
| | - Donald W. Bowden
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC 27157
| | - Barry I. Freedman
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157
| | - Swapan K. Das
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157
- Corresponding author and person to whom reprint requests should be addressed: Swapan K. Das, Ph.D., Section on Endocrinology and Metabolism, Department of Internal Medicine, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, North Carolina 27157, , Telephone: 336-713-6057; Fax: 336-713-7200
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105
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Affiliation(s)
- Jennie Lin
- From the Division of Nephrology and Hypertension, Department of Medicine (J.L.) and Feinberg Cardiovascular Research Institute (J.L.), Northwestern University Feinberg School of Medicine, Chicago, IL; and Division of Cardiovascular Medicine, Department of Medicine, Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia (K.M.)
| | - Kiran Musunuru
- From the Division of Nephrology and Hypertension, Department of Medicine (J.L.) and Feinberg Cardiovascular Research Institute (J.L.), Northwestern University Feinberg School of Medicine, Chicago, IL; and Division of Cardiovascular Medicine, Department of Medicine, Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia (K.M.)
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106
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Lin J, Musunuru K. From Genotype to Phenotype: A Primer on the Functional Follow-up of Genome-Wide Association Studies in Cardiovascular Disease. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2018; 11:e001946. [PMID: 29915816 PMCID: PMC6003539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Genome-wide association studies (GWASs) have implicated many human genomic loci in the development of complex traits. The loci identified by these studies are potentially involved in novel pathways that contribute to disease pathophysiology. However, eventual therapeutic targeting of these pathways relies on bridging the gap between genetic association and function, a task that first requires validation of causal genetic variants, casual genes, and directionality of effect. Executing this task requires basic knowledge of interpreting GWAS results and prioritizing candidates for further study, in addition to understanding the experimental methods available for evaluating candidate variants. Here we review the basic genetic principles of genome-wide association studies, the computational and experimental tools used for identifying causal variants and genes, and salient illustrative examples of how cardiovascular loci have undergone functional investigation.
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Affiliation(s)
- Jennie Lin
- Division of Nephrology and Hypertension, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL
- Feinberg Cardiovascular Research Institute, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Kiran Musunuru
- Division of Cardiovascular Medicine, Department of Medicine, Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
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Argmann CA, Violante S, Dodatko T, Amaro MP, Hagen J, Gillespie VL, Buettner C, Schadt EE, Houten SM. Germline deletion of Krüppel-like factor 14 does not increase risk of diet induced metabolic syndrome in male C57BL/6 mice. Biochim Biophys Acta Mol Basis Dis 2017; 1863:3277-3285. [DOI: 10.1016/j.bbadis.2017.09.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 09/21/2017] [Accepted: 09/25/2017] [Indexed: 01/03/2023]
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108
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Hoffman PL, Saba LM, Vanderlinden LA, Tabakoff B. Voluntary exposure to a toxin: the genetic influence on ethanol consumption. Mamm Genome 2017; 29:128-140. [PMID: 29196862 DOI: 10.1007/s00335-017-9726-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 11/22/2017] [Indexed: 02/07/2023]
Abstract
Ethyl alcohol is a toxin that, when consumed at high levels, produces organ damage and death. One way to prevent or ameliorate this damage in humans is to reduce the exposure of organs to alcohol by reducing alcohol ingestion. Both the propensity to consume large volumes of alcohol and the susceptibility of human organs to alcohol-induced damage exhibit a strong genetic influence. We have developed an integrative genetic/genomic approach to identify transcriptional networks that predispose complex traits, including propensity for alcohol consumption and propensity for alcohol-induced organ damage. In our approach, the phenotype is assessed in a panel of recombinant inbred (RI) rat strains, and quantitative trait locus (QTL) analysis is performed. Transcriptome data from tissues/organs of naïve RI rat strains are used to identify transcriptional networks using Weighted Gene Coexpression Network Analysis (WGCNA). Correlation of the first principal component of transcriptional coexpression modules with the phenotype across the rat strains, and overlap of QTLs for the phenotype and the QTLs for the coexpression modules (module eigengene QTL) provide the criteria for identification of the functionally related groups of genes that contribute to the phenotype (candidate modules). While we previously identified a brain transcriptional module whose QTL overlapped with a QTL for levels of alcohol consumption in HXB/BXH RI rat strains and 12 selected rat lines, this module did not account for all of the genetic variation in alcohol consumption. Our search for QTL overlap and correlation of coexpression modules with phenotype can, however, be applied to any organ in which the transcriptome has been measured, and this represents a holistic approach in the search for genetic contributors to complex traits. Previous work has implicated liver/brain interactions, particularly involving inflammatory/immune processes, as influencing alcohol consumption levels. We have now analyzed the liver transcriptome of the HXB/BXH RI rat panel in relation to the behavioral trait of alcohol consumption. We used RNA-Seq and microarray data to construct liver transcriptional networks, and identified a liver candidate transcriptional coexpression module that explained 24% of the genetic variance in voluntary alcohol consumption. The transcripts in this module focus attention on liver secretory products that influence inflammatory and immune signaling pathways. We propose that these liver secretory products can interact with brain mechanisms that affect alcohol consumption, and targeting these pathways provides a potential approach to reducing high levels of alcohol intake and also protecting the integrity of the liver and other organs.
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Affiliation(s)
- Paula L Hoffman
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences, University of Colorado, Aurora, CO, 80045, USA.,Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Laura M Saba
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences, University of Colorado, Aurora, CO, 80045, USA
| | - Lauren A Vanderlinden
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, CO, 80045, USA
| | - Boris Tabakoff
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences, University of Colorado, Aurora, CO, 80045, USA. .,Department of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, 12850 E. Montview Blvd., Campus Box: C238, Aurora, CO, 80045, USA.
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109
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Martin JS, Xu Z, Reiner AP, Mohlke KL, Sullivan P, Ren B, Hu M, Li Y. HUGIn: Hi-C Unifying Genomic Interrogator. Bioinformatics 2017; 33:3793-3795. [PMID: 28582503 PMCID: PMC5860315 DOI: 10.1093/bioinformatics/btx359] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 05/31/2017] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION High throughput chromatin conformation capture (3C) technologies, such as Hi-C and ChIA-PET, have the potential to elucidate the functional roles of non-coding variants. However, most of published genome-wide unbiased chromatin organization studies have used cultured cell lines, limiting their generalizability. RESULTS We developed a web browser, HUGIn, to visualize Hi-C data generated from 21 human primary tissues and cell lines. HUGIn enables assessment of chromatin contacts both constitutive across and specific to tissue(s) and/or cell line(s) at any genomic loci, including GWAS SNPs, eQTLs and cis-regulatory elements, facilitating the understanding of both GWAS and eQTL results and functional genomics data. AVAILABILITY AND IMPLEMENTATION HUGIn is available at http://yunliweb.its.unc.edu/HUGIn. CONTACT yunli@med.unc.edu or hum@ccf.org. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Joshua S Martin
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Zheng Xu
- Department of Statistics, University of Nebraska, Lincoln, NE, USA,Quantitative Life Sciences Initiative, University of Nebraska, Lincoln, NE, USA
| | - Alex P Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA,Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, USA
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Patrick Sullivan
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA,Department of Medical Epidemiology and Biostatistics, Karolinksa Institutet, Stockholm, Sweden
| | - Bing Ren
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, UCSD Moores Cancer Center, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Ming Hu
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA,To whom correspondence should be addressed. or
| | - Yun Li
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA,Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA,Department of Computer Science, University of North Carolina, Chapel Hill, NC, USA,To whom correspondence should be addressed. or
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110
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Vitali C, Khetarpal SA, Rader DJ. HDL Cholesterol Metabolism and the Risk of CHD: New Insights from Human Genetics. Curr Cardiol Rep 2017; 19:132. [PMID: 29103089 DOI: 10.1007/s11886-017-0940-0] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
PURPOSE OF REVIEW Elevated high-density lipoprotein cholesterol levels in the blood (HDL-C) represent one of the strongest epidemiological surrogates for protection against coronary heart disease (CHD), but recent human genetic and pharmacological intervention studies have raised controversy about the causality of this relationship. Here, we review recent discoveries from human genome studies using new analytic tools as well as relevant animal studies that have both addressed, and in some cases, fueled this controversy. RECENT FINDINGS Methodologic developments in genotyping and sequencing, such as genome-wide association studies (GWAS), exome sequencing, and exome array genotyping, have been applied to the study of HDL-C and risk of CHD in large, multi-ethnic populations. Some of these efforts focused on population-wide variation in common variants have uncovered new polymorphisms at novel loci associated with HDL-C and, in some cases, CHD risk. Other efforts have discovered loss-of-function variants for the first time in genes previously implicated in HDL metabolism through common variant studies or animal models. These studies have allowed the genetic relationship between these pathways, HDL-C and CHD to be explored in humans for the first time through analysis tools such as Mendelian randomization. We explore these discoveries for selected key HDL-C genes CETP, LCAT, LIPG, SCARB1, and novel loci implicated from GWAS including GALNT2, KLF14, and TTC39B. Recent human genetics findings have identified new nodes regulating HDL metabolism while reshaping our current understanding of known candidate genes to HDL and CHD risk through the study of critical variants across model systems. Despite their effect on HDL-C, variants in many of the reviewed genes were found to lack any association with CHD. These data collectively indicate that HDL-C concentration, which represents a static picture of a very dynamic and heterogeneous metabolic milieu, is unlikely to be itself causally protective against CHD. In this context, human genetics represent an extremely valuable tool to further explore the biological mechanisms regulating HDL metabolism and investigate what role, if any, HDL plays in the pathogenesis of CHD.
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Affiliation(s)
- Cecilia Vitali
- Perelman School of Medicine at the University of Pennsylvania, 11-162 TRC, 3400 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Sumeet A Khetarpal
- Perelman School of Medicine at the University of Pennsylvania, 11-162 TRC, 3400 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Daniel J Rader
- Perelman School of Medicine at the University of Pennsylvania, 11-162 TRC, 3400 Civic Center Blvd, Philadelphia, PA, 19104, USA. .,Departments of Genetics and Medicine, Cardiovascular Institute, and Institute for Translational Medicine and Therapeutics, Perelman School of Medicine at the University of Pennsylvania, 11-125 TRC, 3400 Civic Center Blvd, Philadelphia, PA, 19104, USA.
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111
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Sajuthi SP, Sharma NK, Comeau ME, Chou JW, Bowden DW, Freedman BI, Langefeld CD, Parks JS, Das SK. Genetic regulation of adipose tissue transcript expression is involved in modulating serum triglyceride and HDL-cholesterol. Gene 2017; 632:50-58. [PMID: 28844666 DOI: 10.1016/j.gene.2017.08.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 07/06/2017] [Accepted: 08/23/2017] [Indexed: 10/19/2022]
Abstract
Dyslipidemia is a major contributor to the increased cardiovascular disease and mortality associated with obesity and type 2 diabetes. We hypothesized that variation in expression of adipose tissue transcripts is associated with serum lipid concentrations in African Americans (AAs), and common genetic variants regulate expression levels of these transcripts. Fasting serum lipid levels, genome-wide transcript expression profiles of subcutaneous adipose tissue, and genome-wide SNP genotypes were analyzed in a cohort of non-diabetic AAs (N=250). Serum triglyceride (TRIG) and high density lipoprotein-cholesterol (HDL-C) levels were associated (FDR<0.01) with expression level of 1021 and 1875 adipose tissue transcripts, respectively, but none associated with total cholesterol or LDL-C levels. Serum HDL-C-associated transcripts were enriched for salient biological pathways, including branched-chain amino acid degradation, and oxidative phosphorylation. Genes in immuno-inflammatory pathways were activated among individuals with higher serum TRIG levels. We identified significant cis-regulatory SNPs (cis-eSNPs) for 449 serum lipid-associated transcripts in adipose tissue. The cis-eSNPs of 12 genes were nominally associated (p<0.001) with serum lipid level in genome wide association studies in Global Lipids Genetics Consortium (GLGC) cohorts. Allelic effect direction of cis-eSNPs on expression of MARCH2, BEST1 and TMEM258 matched with effect direction of these SNP alleles on serum TRIG or HDL-C levels in GLGC cohorts. These data suggest that expressions of serum lipid-associated transcripts in adipose tissue are dependent on common cis-eSNPs in African Americans. Thus, genetically-mediated transcriptional regulation in adipose tissue may play a role in reducing HDL-C and increasing TRIG in serum.
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Affiliation(s)
- Satria P Sajuthi
- Department of Biostatistical Sciences, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC 27157, United States
| | - Neeraj K Sharma
- Department of Internal Medicine, Section on Endocrinology and Metabolism, Wake Forest School of Medicine, Winston-Salem, NC 27157, United States
| | - Mary E Comeau
- Department of Biostatistical Sciences, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC 27157, United States
| | - Jeff W Chou
- Department of Biostatistical Sciences, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC 27157, United States
| | - Donald W Bowden
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC 27157, United States
| | - Barry I Freedman
- Department of Internal Medicine, Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, NC 27157, United States
| | - Carl D Langefeld
- Department of Biostatistical Sciences, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC 27157, United States
| | - John S Parks
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, United States
| | - Swapan K Das
- Department of Internal Medicine, Section on Endocrinology and Metabolism, Wake Forest School of Medicine, Winston-Salem, NC 27157, United States.
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112
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Spracklen CN, Chen P, Kim YJ, Wang X, Cai H, Li S, Long J, Wu Y, Wang YX, Takeuchi F, Wu JY, Jung KJ, Hu C, Akiyama K, Zhang Y, Moon S, Johnson TA, Li H, Dorajoo R, He M, Cannon ME, Roman TS, Salfati E, Lin KH, Guo X, Sheu WHH, Absher D, Adair LS, Assimes TL, Aung T, Cai Q, Chang LC, Chen CH, Chien LH, Chuang LM, Chuang SC, Du S, Fan Q, Fann CSJ, Feranil AB, Friedlander Y, Gordon-Larsen P, Gu D, Gui L, Guo Z, Heng CK, Hixson J, Hou X, Hsiung CA, Hu Y, Hwang MY, Hwu CM, Isono M, Juang JMJ, Khor CC, Kim YK, Koh WP, Kubo M, Lee IT, Lee SJ, Lee WJ, Liang KW, Lim B, Lim SH, Liu J, Nabika T, Pan WH, Peng H, Quertermous T, Sabanayagam C, Sandow K, Shi J, Sun L, Tan PC, Tan SP, Taylor KD, Teo YY, Toh SA, Tsunoda T, van Dam RM, Wang A, Wang F, Wang J, Wei WB, Xiang YB, Yao J, Yuan JM, Zhang R, Zhao W, Chen YDI, Rich SS, Rotter JI, Wang TD, Wu T, Lin X, Han BG, Tanaka T, Cho YS, Katsuya T, Jia W, Jee SH, Chen YT, Kato N, Jonas JB, Cheng CY, Shu XO, He J, Zheng W, Wong TY, Huang W, Kim BJ, Tai ES, Mohlke KL, Sim X. Association analyses of East Asian individuals and trans-ancestry analyses with European individuals reveal new loci associated with cholesterol and triglyceride levels. Hum Mol Genet 2017; 26:1770-1784. [PMID: 28334899 DOI: 10.1093/hmg/ddx062] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 02/16/2017] [Indexed: 12/28/2022] Open
Abstract
Large-scale meta-analyses of genome-wide association studies (GWAS) have identified >175 loci associated with fasting cholesterol levels, including total cholesterol (TC), high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), and triglycerides (TG). With differences in linkage disequilibrium (LD) structure and allele frequencies between ancestry groups, studies in additional large samples may detect new associations. We conducted staged GWAS meta-analyses in up to 69,414 East Asian individuals from 24 studies with participants from Japan, the Philippines, Korea, China, Singapore, and Taiwan. These meta-analyses identified (P < 5 × 10-8) three novel loci associated with HDL-C near CD163-APOBEC1 (P = 7.4 × 10-9), NCOA2 (P = 1.6 × 10-8), and NID2-PTGDR (P = 4.2 × 10-8), and one novel locus associated with TG near WDR11-FGFR2 (P = 2.7 × 10-10). Conditional analyses identified a second signal near CD163-APOBEC1. We then combined results from the East Asian meta-analysis with association results from up to 187,365 European individuals from the Global Lipids Genetics Consortium in a trans-ancestry meta-analysis. This analysis identified (log10Bayes Factor ≥6.1) eight additional novel lipid loci. Among the twelve total loci identified, the index variants at eight loci have demonstrated at least nominal significance with other metabolic traits in prior studies, and two loci exhibited coincident eQTLs (P < 1 × 10-5) in subcutaneous adipose tissue for BPTF and PDGFC. Taken together, these analyses identified multiple novel lipid loci, providing new potential therapeutic targets.
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Affiliation(s)
| | - Peng Chen
- Saw Swee Hock School of Public Health, National University Health System, National University of Singapore, Singapore, Singapore.,Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun, China
| | - Young Jin Kim
- Division of Structural and Functional Genomics, Center for Genome Science, Korean National Institute of Health, Osong, Chungchungbuk-do, South Korea
| | - Xu Wang
- Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Hui Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Shengxu Li
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Ying Wu
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Ya Xing Wang
- Beijing Institute of Ophthalmology, Beijing Ophthalmology and Visual Science Key Lab, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | | | - Jer-Yuarn Wu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.,School of Chinese Medicine, China Medical University, Taichung, Taiwan
| | - Keum-Ji Jung
- Institute for Health Promotion, Graduate School of Public Health, Yonsei University, Seoul, South Korea
| | - Cheng Hu
- Shanghai Diabetes Institute, Shanghai Jiaotong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Koichi Akiyama
- National Center for Global Health and Medicine, Tokyo, Japan
| | - Yonghong Zhang
- Department of Epidemiology, School of Public Health and Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Medical College of Soochow University, Suzhou, China
| | - Sanghoon Moon
- Division of Structural and Functional Genomics, Center for Genome Science, Korean National Institute of Health, Osong, Chungchungbuk-do, South Korea
| | - Todd A Johnson
- Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Huaixing Li
- Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Shanghai, China
| | - Rajkumar Dorajoo
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Meian He
- Department of Occupational and Environmental Health and State Key Laboratory of Environmental Health for Incubating, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Maren E Cannon
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Tamara S Roman
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Elias Salfati
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Keng-Hung Lin
- Department of Ophthalmology, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Xiuqing Guo
- Department of Pediatrics, Institute for Translational Genomics and Population Sciences, LABioMed at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Wayne H H Sheu
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan.,School of Medicine, National Yang-Ming University, Taipei, Taiwan.,School of Medicine, National Defense Medical Center, Taipei, Taiwan.,Institute of Medical Technology, National Chung-Hsing University, Taichung, Taiwan
| | - Devin Absher
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Linda S Adair
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA
| | | | - Tin Aung
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore.,Duke-NUS Medical School Singapore, Singapore, Singapore.,Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Li-Ching Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Chien-Hsiun Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.,School of Chinese Medicine, China Medical University, Taichung, Taiwan
| | - Li-Hsin Chien
- Institute of Population Health Sciences, National Health Research Institutes, Miaoli, Taiwan
| | - Lee-Ming Chuang
- Division of Endocrinology & Metabolism, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan.,College of Medicine, National Taiwan University, Taipei, Taiwan.,Institute of Preventive Medicine, School of Public Health, National Taiwan University, Taipei, Taiwan
| | - Shu-Chun Chuang
- Institute of Population Health Sciences, National Health Research Institutes, Miaoli, Taiwan
| | - Shufa Du
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA.,Carolina Population Center, University of North Carolina, Chapel Hill, NC, USA
| | - Qiao Fan
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | - Cathy S J Fann
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Alan B Feranil
- USC-Office of Population Studies Foundation, Inc, University of San Carlos, Cebu City, Philippines.,Department of Anthropology, Sociology, and History, University of San Carlos, Cebu City, Philippines
| | - Yechiel Friedlander
- Unit of Epidemiology, Hebrew University-Hadassah Braun School of Public Health, Jerusalem, Israel
| | - Penny Gordon-Larsen
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA.,Carolina Population Center, University of North Carolina, Chapel Hill, NC, USA
| | - Dongfeng Gu
- Department of Epidemiology and Population Genetics, Fuwai Hospital, Beijing, China
| | - Lixuan Gui
- Department of Occupational and Environmental Health and State Key Laboratory of Environmental Health for Incubating, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Zhirong Guo
- Department of Epidemiology, School of Public Health and Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Medical College of Soochow University, Suzhou, China
| | - Chew-Kiat Heng
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Khoo Teck Puat-National University Children's Medical Institute, National University Health System, Singapore, Singapore
| | - James Hixson
- Human Genetics Center, University of Texas School of Public Health, Houston, TX, USA
| | - Xuhong Hou
- Shanghai Diabetes Institute, Shanghai Jiaotong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Chao Agnes Hsiung
- Institute of Population Health Sciences, National Health Research Institutes, Miaoli, Taiwan
| | - Yao Hu
- Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Shanghai, China
| | - Mi Yeong Hwang
- Division of Structural and Functional Genomics, Center for Genome Science, Korean National Institute of Health, Osong, Chungchungbuk-do, South Korea
| | - Chii-Min Hwu
- School of Medicine, National Yang-Ming University, Taipei, Taiwan.,Section of Endocrinology and Metabolism, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Masato Isono
- National Center for Global Health and Medicine, Tokyo, Japan
| | - Jyh-Ming Jimmy Juang
- College of Medicine, National Taiwan University, Taipei, Taiwan.,Cardiovascular Center and Division of Cardiology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Chiea-Chuen Khor
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore.,Department of Biochemistry, National University of Singapore, Singapore, Singapore
| | - Yun Kyoung Kim
- Division of Structural and Functional Genomics, Center for Genome Science, Korean National Institute of Health, Osong, Chungchungbuk-do, South Korea
| | - Woon-Puay Koh
- Saw Swee Hock School of Public Health, National University Health System, National University of Singapore, Singapore, Singapore.,Duke-NUS Medical School Singapore, Singapore, Singapore
| | - Michiaki Kubo
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - I-Te Lee
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan.,School of Medicine, National Yang-Ming University, Taipei, Taiwan.,School of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Sun-Ju Lee
- Institute for Health Promotion, Graduate School of Public Health, Yonsei University, Seoul, South Korea
| | - Wen-Jane Lee
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan.,Department of Social Work, Tunghai University, Taichung, Taiwan
| | - Kae-Woei Liang
- School of Medicine, National Yang-Ming University, Taipei, Taiwan.,Cardiovascular Center, Taichung Veterans General Hospital, Taichung, Taiwan.,Department of Medicine, China Medical University, Taichung, Taiwan
| | - Blanche Lim
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | - Sing-Hui Lim
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | - Jianjun Liu
- Saw Swee Hock School of Public Health, National University Health System, National University of Singapore, Singapore, Singapore.,Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Toru Nabika
- Department of Functional Pathology, Shimane University School of Medicine, Izumo, Japan
| | - Wen-Harn Pan
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Hao Peng
- Department of Epidemiology, School of Public Health and Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Medical College of Soochow University, Suzhou, China
| | - Thomas Quertermous
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Charumathi Sabanayagam
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore.,Duke-NUS Medical School Singapore, Singapore, Singapore
| | - Kevin Sandow
- Department of Pediatrics, Institute for Translational Genomics and Population Sciences, LABioMed at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Jinxiu Shi
- Department of Genetics, Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center and Shanghai Industrial Technology Institute, Shanghai, China
| | - Liang Sun
- Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Shanghai, China
| | - Pok Chien Tan
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | - Shu-Pei Tan
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | - Kent D Taylor
- Department of Pediatrics, Institute for Translational Genomics and Population Sciences, LABioMed at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Yik-Ying Teo
- Saw Swee Hock School of Public Health, National University Health System, National University of Singapore, Singapore, Singapore.,Life Sciences Institute, National University of Singapore, Singapore, Singapore.,Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore.,NUS Graduate School for Integrative Science and Engineering, National University of Singapore, Singapore, Singapore.,Department of Statistics and Applied Probability, National University of Singapore, Singapore, Singapore
| | - Sue-Anne Toh
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Tatsuhiko Tsunoda
- Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Department of Medical Science Mathematics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Rob M van Dam
- Saw Swee Hock School of Public Health, National University Health System, National University of Singapore, Singapore, Singapore
| | - Aili Wang
- Department of Epidemiology, School of Public Health and Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Medical College of Soochow University, Suzhou, China
| | - Feijie Wang
- Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Shanghai, China
| | - Jie Wang
- Shanghai Diabetes Institute, Shanghai Jiaotong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Wen Bin Wei
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Beijing Ophthalmology and Visual Science Key Lab, Beijing Key Laboratory of Intraocular Tumor Diagnosis and Treatment, Capital Medical University, Beijing, China
| | - Yong-Bing Xiang
- Department of Epidemiology, Shanghai Cancer Institute, Shanghai, China
| | - Jie Yao
- Department of Pediatrics, Institute for Translational Genomics and Population Sciences, LABioMed at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Jian-Min Yuan
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA.,Division of Cancer Control and Population Sciences, University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA
| | - Rong Zhang
- Shanghai Diabetes Institute, Shanghai Jiaotong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Wanting Zhao
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore.,Duke-NUS Medical School Singapore, Singapore, Singapore
| | - Yii-Der Ida Chen
- Department of Pediatrics, Institute for Translational Genomics and Population Sciences, LABioMed at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Jerome I Rotter
- Department of Pediatrics, Institute for Translational Genomics and Population Sciences, LABioMed at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Tzung-Dau Wang
- College of Medicine, National Taiwan University, Taipei, Taiwan.,Cardiovascular Center and Division of Cardiology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Tangchun Wu
- Department of Occupational and Environmental Health and State Key Laboratory of Environmental Health for Incubating, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xu Lin
- Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Shanghai, China
| | - Bok-Ghee Han
- Center for Genome Science, Korean National Institute of Health, Osong, Chungchungbuk-do, South Korea
| | - Toshihiro Tanaka
- Laboratory for Cardiovascular Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Department of Human Genetics and Disease Diversity, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yoon Shin Cho
- Department of Biomedical Science, Hallym University, Chuncheon, South Korea
| | - Tomohiro Katsuya
- Department of Clinical Gene Therapy, Osaka University Graduate School of Medicine, Suita, Japan
| | - Weiping Jia
- Shanghai Diabetes Institute, Shanghai Jiaotong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Sun-Ha Jee
- Institute for Health Promotion, Graduate School of Public Health, Yonsei University, Seoul, South Korea
| | - Yuan-Tsong Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Norihiro Kato
- National Center for Global Health and Medicine, Tokyo, Japan
| | - Jost B Jonas
- Beijing Institute of Ophthalmology, Beijing Ophthalmology and Visual Science Key Lab, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China.,Department of Ophthalmology, Medical Faculty Mannheim of the Ruprecht-Karls-University of Heidelberg, Mannheim, Germany
| | - Ching-Yu Cheng
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore.,Duke-NUS Medical School Singapore, Singapore, Singapore.,Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Jiang He
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Tien-Yin Wong
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore.,Duke-NUS Medical School Singapore, Singapore, Singapore.,Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Wei Huang
- Department of Genetics, Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center and Shanghai Industrial Technology Institute, Shanghai, China
| | - Bong-Jo Kim
- Division of Structural and Functional Genomics, Center for Genome Science, Korean National Institute of Health, Osong, Chungchungbuk-do, South Korea
| | - E-Shyong Tai
- Saw Swee Hock School of Public Health, National University Health System, National University of Singapore, Singapore, Singapore.,Duke-NUS Medical School Singapore, Singapore, Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Xueling Sim
- Saw Swee Hock School of Public Health, National University Health System, National University of Singapore, Singapore, Singapore
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113
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Trans-ancestry Fine Mapping and Molecular Assays Identify Regulatory Variants at the ANGPTL8 HDL-C GWAS Locus. G3-GENES GENOMES GENETICS 2017; 7:3217-3227. [PMID: 28754724 PMCID: PMC5592946 DOI: 10.1534/g3.117.300088] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Recent genome-wide association studies (GWAS) have identified variants associated with high-density lipoprotein cholesterol (HDL-C) located in or near the ANGPTL8 gene. Given the extensive sharing of GWAS loci across populations, we hypothesized that at least one shared variant at this locus affects HDL-C. The HDL-C–associated variants are coincident with expression quantitative trait loci for ANGPTL8 and DOCK6 in subcutaneous adipose tissue; however, only ANGPTL8 expression levels are associated with HDL-C levels. We identified a 400-bp promoter region of ANGPTL8 and enhancer regions within 5 kb that contribute to regulating expression in liver and adipose. To identify variants functionally responsible for the HDL-C association, we performed fine-mapping analyses and selected 13 candidate variants that overlap putative regulatory regions to test for allelic differences in regulatory function. Of these variants, rs12463177-G increased transcriptional activity (1.5-fold, P = 0.004) and showed differential protein binding. Six additional variants (rs17699089, rs200788077, rs56322906, rs3760782, rs737337, and rs3745683) showed evidence of allelic differences in transcriptional activity and/or protein binding. Taken together, these data suggest a regulatory mechanism at the ANGPTL8 HDL-C GWAS locus involving tissue-selective expression and at least one functional variant.
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114
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Brænne I, Willenborg C, Tragante V, Kessler T, Zeng L, Reiz B, Kleinecke M, von Ameln S, Willer CJ, Laakso M, Wild PS, Zeller T, Wallentin L, Franks PW, Salomaa V, Dehghan A, Meitinger T, Samani NJ, Asselbergs FW, Erdmann J, Schunkert H. A genomic exploration identifies mechanisms that may explain adverse cardiovascular effects of COX-2 inhibitors. Sci Rep 2017; 7:10252. [PMID: 28860667 PMCID: PMC5579257 DOI: 10.1038/s41598-017-10928-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 08/16/2017] [Indexed: 01/06/2023] Open
Abstract
Cyclooxygenase-2 inhibitors (coxibs) are characterized by multiple molecular off-target effects and increased coronary artery disease (CAD) risk. Here, we systematically explored common variants of genes representing molecular targets of coxibs for association with CAD. Given a broad spectrum of pleiotropic effects of coxibs, our intention was to narrow potential mechanisms affecting CAD risk as we hypothesized that the affected genes may also display genomic signals of coronary disease risk. A Drug Gene Interaction Database search identified 47 gene products to be affected by coxibs. We traced association signals in 200-kb regions surrounding these genes in 84,813 CAD cases and 202,543 controls. Based on a threshold of 1 × 10−5 (Bonferroni correction for 3131 haplotype blocks), four gene loci yielded significant associations. The lead SNPs were rs7270354 (MMP9), rs4888383 (BCAR1), rs6905288 (VEGFA1), and rs556321 (CACNA1E). By additional genotyping, rs7270354 at MMP9 and rs4888383 at BCAR1 also reached the established GWAS threshold for genome-wide significance. The findings demonstrate overlap of genes affected by coxibs and those mediating CAD risk and points to further mechanisms, which are potentially responsible for coxib-associated CAD risk. The novel approach furthermore suggests that genetic studies may be useful to explore the clinical relevance of off-target drug effects.
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Affiliation(s)
- Ingrid Brænne
- Institute for Cardiogenetics, University of Lübeck, 23562, Lübeck, Germany.,DZHK (German Research Center for Cardiovascular Research), partner site Hamburg/Lübeck/Kiel, 23562, Lübeck, Germany.,University Heart Center Lübeck, 23562, Lübeck, Germany
| | | | - Vinicius Tragante
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, 3584, Utrecht, The Netherlands
| | - Thorsten Kessler
- Deutsches Herzzentrum München, Technische Universität München, 80636, München, Germany
| | - Lingyao Zeng
- Deutsches Herzzentrum München, Technische Universität München, 80636, München, Germany
| | - Benedikt Reiz
- Institute for Cardiogenetics, University of Lübeck, 23562, Lübeck, Germany.,DZHK (German Research Center for Cardiovascular Research), partner site Hamburg/Lübeck/Kiel, 23562, Lübeck, Germany.,University Heart Center Lübeck, 23562, Lübeck, Germany
| | - Mariana Kleinecke
- Institute for Cardiogenetics, University of Lübeck, 23562, Lübeck, Germany.,DZHK (German Research Center for Cardiovascular Research), partner site Hamburg/Lübeck/Kiel, 23562, Lübeck, Germany.,University Heart Center Lübeck, 23562, Lübeck, Germany
| | - Simon von Ameln
- Deutsches Herzzentrum München, Technische Universität München, 80636, München, Germany
| | - Cristen J Willer
- University of Michigan, Dept of Biostatistics, 1415 Washington Hts, Ann Arbor, MI, 48104, USA
| | - Markku Laakso
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland and Kuopio University Hospital, 70210, Kuopio, Finland
| | - Philipp S Wild
- Preventive Cardiology and Preventive Medicine, Center for Cardiology, University Medical Center Mainz, Mainz, Germany.,Center for Thrombosis and Hemostasis, University Medical Center Mainz, Mainz, Germany.,DZHK (German Center for Cardiovascular Research), Partner Site RhineMain, Mainz, Germany
| | - Tanja Zeller
- DZHK (German Research Center for Cardiovascular Research), partner site Hamburg/Lübeck/Kiel, 23562, Lübeck, Germany.,Department of General and Interventional Cardiology, University Heart Center Hamburg-Eppendorf, Hamburg, Germany
| | - Lars Wallentin
- Uppsala Clinical Research Center, Uppsala Science Park, MTC, SE-752 37, Uppsala, Sweden
| | - Paul W Franks
- Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Lund University, Skåne University Hospital Malmö, Malmö, Sweden
| | - Veikko Salomaa
- THL-National Institute for Health and Welfare, POB 30, Mannerheimintie 166, FI-00271, Helsinki, Finland
| | - Abbas Dehghan
- Department of Epidemiology, Erasmus University Medical Center, 3000 CA, Rotterdam, The Netherlands
| | - Thomas Meitinger
- Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany.,DZHK (German Center for Cardiovascular Research), partner site Munich Heart Alliance, 80636, Munich, Germany.,Institute of Human Genetics, Technische Universität München, 81675, Munich, Germany
| | - Nilesh J Samani
- Deparment of Cardiovascular Sciences University of Leicester and NIHR Leicester Cardiovascular Biomedical Research Unit, Glenfield Hospital, Leicester, LE3 9QP, UK
| | - Folkert W Asselbergs
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, 3584, Utrecht, The Netherlands.,Institute of Cardiovascular Science, faculty of Population Health Sciences, University College London, London, United Kingdom
| | - Jeanette Erdmann
- Institute for Cardiogenetics, University of Lübeck, 23562, Lübeck, Germany. .,DZHK (German Research Center for Cardiovascular Research), partner site Hamburg/Lübeck/Kiel, 23562, Lübeck, Germany. .,University Heart Center Lübeck, 23562, Lübeck, Germany.
| | - Heribert Schunkert
- Deutsches Herzzentrum München, Technische Universität München, 80636, München, Germany.,DZHK (German Center for Cardiovascular Research), partner site Munich Heart Alliance, 80636, Munich, Germany
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115
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Epistatic Networks Jointly Influence Phenotypes Related to Metabolic Disease and Gene Expression in Diversity Outbred Mice. Genetics 2017; 206:621-639. [PMID: 28592500 PMCID: PMC5499176 DOI: 10.1534/genetics.116.198051] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 04/03/2017] [Indexed: 12/20/2022] Open
Abstract
In this study, Tyler et al. analyzed the complex genetic architecture of metabolic disease-related traits using the Diversity Outbred mouse population Genetic studies of multidimensional phenotypes can potentially link genetic variation, gene expression, and physiological data to create multi-scale models of complex traits. The challenge of reducing these data to specific hypotheses has become increasingly acute with the advent of genome-scale data resources. Multi-parent populations derived from model organisms provide a resource for developing methods to understand this complexity. In this study, we simultaneously modeled body composition, serum biomarkers, and liver transcript abundances from 474 Diversity Outbred mice. This population contained both sexes and two dietary cohorts. Transcript data were reduced to functional gene modules with weighted gene coexpression network analysis (WGCNA), which were used as summary phenotypes representing enriched biological processes. These module phenotypes were jointly analyzed with body composition and serum biomarkers in a combined analysis of pleiotropy and epistasis (CAPE), which inferred networks of epistatic interactions between quantitative trait loci that affect one or more traits. This network frequently mapped interactions between alleles of different ancestries, providing evidence of both genetic synergy and redundancy between haplotypes. Furthermore, a number of loci interacted with sex and diet to yield sex-specific genetic effects and alleles that potentially protect individuals from the effects of a high-fat diet. Although the epistatic interactions explained small amounts of trait variance, the combination of directional interactions, allelic specificity, and high genomic resolution provided context to generate hypotheses for the roles of specific genes in complex traits. Our approach moves beyond the cataloging of single loci to infer genetic networks that map genetic etiology by simultaneously modeling all phenotypes.
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116
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Manning A, Highland HM, Gasser J, Sim X, Tukiainen T, Fontanillas P, Grarup N, Rivas MA, Mahajan A, Locke AE, Cingolani P, Pers TH, Viñuela A, Brown AA, Wu Y, Flannick J, Fuchsberger C, Gamazon ER, Gaulton KJ, Im HK, Teslovich TM, Blackwell TW, Bork-Jensen J, Burtt NP, Chen Y, Green T, Hartl C, Kang HM, Kumar A, Ladenvall C, Ma C, Moutsianas L, Pearson RD, Perry JR, Rayner NW, Robertson NR, Scott LJ, van de Bunt M, Eriksson JG, Jula A, Koskinen S, Lehtimäki T, Palotie A, Raitakari OT, Jacobs SB, Wessel J, Chu AY, Scott RA, Goodarzi MO, Blancher C, Buck G, Buck D, Chines PS, Gabriel S, Gjesing AP, Groves CJ, Hollensted M, Huyghe JR, Jackson AU, Jun G, Justesen JM, Mangino M, Murphy J, Neville M, Onofrio R, Small KS, Stringham HM, Trakalo J, Banks E, Carey J, Carneiro MO, DePristo M, Farjoun Y, Fennell T, Goldstein JI, Grant G, Hrabé de Angelis M, Maguire J, Neale BM, Poplin R, Purcell S, Schwarzmayr T, Shakir K, Smith JD, Strom TM, Wieland T, Lindstrom J, Brandslund I, Christensen C, Surdulescu GL, Lakka TA, Doney AS, Nilsson P, Wareham NJ, Langenberg C, Varga TV, Franks PW, Rolandsson O, Rosengren AH, Farook VS, Thameem F, Puppala S, Kumar S, Lehman DM, Jenkinson CP, Curran JE, Hale DE, Fowler SP, Arya R, DeFronzo RA, Abboud HE, Syvänen AC, Hicks PJ, Palmer ND, Ng MC, Bowden DW, Freedman BI, Esko T, Mägi R, Milani L, Mihailov E, Metspalu A, Narisu N, Kinnunen L, Bonnycastle LL, Swift A, Pasko D, Wood AR, Fadista J, Pollin TI, Barzilai N, Atzmon G, Glaser B, Thorand B, Strauch K, Peters A, Roden M, Müller-Nurasyid M, Liang L, Kriebel J, Illig T, Grallert H, Gieger C, Meisinger C, Lannfelt L, Musani SK, Griswold M, Taylor HA, Wilson G, Correa A, Oksa H, Scott WR, Afzal U, Tan ST, Loh M, Chambers JC, Sehmi J, Kooner JS, Lehne B, Cho YS, Lee JY, Han BG, Käräjämäki A, Qi Q, Qi L, Huang J, Hu FB, Melander O, Orho-Melander M, Below JE, Aguilar D, Wong TY, Liu J, Khor CC, Chia KS, Lim WY, Cheng CY, Chan E, Tai ES, Aung T, Linneberg A, Isomaa B, Meitinger T, Tuomi T, Hakaste L, Kravic J, Jørgensen ME, Lauritzen T, Deloukas P, Stirrups KE, Owen KR, Farmer AJ, Frayling TM, O'Rahilly SP, Walker M, Levy JC, Hodgkiss D, Hattersley AT, Kuulasmaa T, Stančáková A, Barroso I, Bharadwaj D, Chan J, Chandak GR, Daly MJ, Donnelly PJ, Ebrahim SB, Elliott P, Fingerlin T, Froguel P, Hu C, Jia W, Ma RC, McVean G, Park T, Prabhakaran D, Sandhu M, Scott J, Sladek R, Tandon N, Teo YY, Zeggini E, Watanabe RM, Koistinen HA, Kesaniemi YA, Uusitupa M, Spector TD, Salomaa V, Rauramaa R, Palmer CN, Prokopenko I, Morris AD, Bergman RN, Collins FS, Lind L, Ingelsson E, Tuomilehto J, Karpe F, Groop L, Jørgensen T, Hansen T, Pedersen O, Kuusisto J, Abecasis G, Bell GI, Blangero J, Cox NJ, Duggirala R, Seielstad M, Wilson JG, Dupuis J, Ripatti S, Hanis CL, Florez JC, Mohlke KL, Meigs JB, Laakso M, Morris AP, Boehnke M, Altshuler D, McCarthy MI, Gloyn AL, Lindgren CM. A Low-Frequency Inactivating AKT2 Variant Enriched in the Finnish Population Is Associated With Fasting Insulin Levels and Type 2 Diabetes Risk. Diabetes 2017; 66:2019-2032. [PMID: 28341696 PMCID: PMC5482074 DOI: 10.2337/db16-1329] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 03/13/2017] [Indexed: 01/04/2023]
Abstract
To identify novel coding association signals and facilitate characterization of mechanisms influencing glycemic traits and type 2 diabetes risk, we analyzed 109,215 variants derived from exome array genotyping together with an additional 390,225 variants from exome sequence in up to 39,339 normoglycemic individuals from five ancestry groups. We identified a novel association between the coding variant (p.Pro50Thr) in AKT2 and fasting plasma insulin (FI), a gene in which rare fully penetrant mutations are causal for monogenic glycemic disorders. The low-frequency allele is associated with a 12% increase in FI levels. This variant is present at 1.1% frequency in Finns but virtually absent in individuals from other ancestries. Carriers of the FI-increasing allele had increased 2-h insulin values, decreased insulin sensitivity, and increased risk of type 2 diabetes (odds ratio 1.05). In cellular studies, the AKT2-Thr50 protein exhibited a partial loss of function. We extend the allelic spectrum for coding variants in AKT2 associated with disorders of glucose homeostasis and demonstrate bidirectional effects of variants within the pleckstrin homology domain of AKT2.
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Affiliation(s)
- Alisa Manning
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- Center for Human Genetic Research, Department of Medicine, Massachusetts General Hospital, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
| | - Heather M. Highland
- Human Genetics Center, The University of Texas MD Anderson Cancer Center and The University of Texas Health Science Center at Houston Graduate School of Biomedical Sciences, Houston, TX
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Jessica Gasser
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
| | - Xueling Sim
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, MI
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Taru Tukiainen
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA
- Department of Genetics, Harvard Medical School, Boston, MA
| | - Pierre Fontanillas
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- 23andMe, Mountain View, CA
| | - Niels Grarup
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Manuel A. Rivas
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, U.K
| | - Anubha Mahajan
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, U.K
| | - Adam E. Locke
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Pablo Cingolani
- School of Computer Science, McGill University, Montreal, Canada
- McGill University and Génome Québec Innovation Centre, Montreal, Canada
| | - Tune H. Pers
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Divisions of Endocrinology and Genetics and Genomics and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Ana Viñuela
- Department of Twin Research & Genetic Epidemiology, King’s College London, London, U.K
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland
| | - Andrew A. Brown
- Wellcome Trust Sanger Institute, Hinxton, U.K
- Norwegian Centre for Mental Disorders Research and KG Jebsen Center for Psychosis Research, Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Ying Wu
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Jason Flannick
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA
| | - Christian Fuchsberger
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Eric R. Gamazon
- Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL
- Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Kyle J. Gaulton
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, U.K
- Department of Pediatrics, University of California, San Diego, La Jolla, CA
| | - Hae Kyung Im
- Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL
| | - Tanya M. Teslovich
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Thomas W. Blackwell
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Jette Bork-Jensen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Noël P. Burtt
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
| | - Yuhui Chen
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, U.K
| | - Todd Green
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
| | - Christopher Hartl
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
| | - Hyun Min Kang
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Ashish Kumar
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, U.K
- Chronic Disease Epidemiology Unit, Swiss Tropical and Public Health Institute, University of Basel, Basel, Switzerland
| | - Claes Ladenvall
- Diabetes and Endocrinology Unit, Department of Clinical Sciences Malmö, Lund University Diabetes Centre, Malmö, Sweden
| | - Clement Ma
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Loukas Moutsianas
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, U.K
| | - Richard D. Pearson
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, U.K
| | - John R.B. Perry
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, U.K
- Genetics of Complex Traits, University of Exeter Medical School, Exeter, U.K
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, U.K
| | - N. William Rayner
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, U.K
- Oxford Centre for Diabetes, Endocrinology & Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, U.K
- Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton, U.K
| | - Neil R. Robertson
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, U.K
- Oxford Centre for Diabetes, Endocrinology & Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, U.K
| | - Laura J. Scott
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Martijn van de Bunt
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, U.K
- Oxford Centre for Diabetes, Endocrinology & Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, U.K
| | - Johan G. Eriksson
- Department of General Practice and Primary Health Care, University of Helsinki, Helsinki, Finland
- Unit of General Practice, Helsinki University Central Hospital, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
- Vaasa Central Hospital, Vaasa, Finland
- Department of Health, National Institute for Health and Welfare, Helsinki, Finland
| | - Antti Jula
- Department of Health, National Institute for Health and Welfare, Helsinki, Finland
| | - Seppo Koskinen
- Department of Health, National Institute for Health and Welfare, Helsinki, Finland
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, University of Tampere School of Medicine, Tampere, Finland
| | - Aarno Palotie
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- Center for Human Genetic Research, Department of Medicine, Massachusetts General Hospital, Boston, MA
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Olli T. Raitakari
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
| | | | - Jennifer Wessel
- Department of Epidemiology, Fairbanks School of Public Health, Indianapolis, IN
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN
| | - Audrey Y. Chu
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA
| | - Robert A. Scott
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, U.K
| | - Mark O. Goodarzi
- Division of Endocrinology, Diabetes & Metabolism, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Christine Blancher
- High-Throughput Genomics, Oxford Genomics Centre, Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, U.K
| | - Gemma Buck
- High-Throughput Genomics, Oxford Genomics Centre, Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, U.K
| | - David Buck
- High-Throughput Genomics, Oxford Genomics Centre, Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, U.K
| | - Peter S. Chines
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Stacey Gabriel
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
| | - Anette P. Gjesing
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Christopher J. Groves
- Oxford Centre for Diabetes, Endocrinology & Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, U.K
| | - Mette Hollensted
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jeroen R. Huyghe
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Anne U. Jackson
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Goo Jun
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Johanne Marie Justesen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Massimo Mangino
- Department of Twin Research & Genetic Epidemiology, King’s College London, London, U.K
| | - Jacquelyn Murphy
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
| | - Matt Neville
- Oxford Centre for Diabetes, Endocrinology & Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, U.K
| | - Robert Onofrio
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
| | - Kerrin S. Small
- Department of Twin Research & Genetic Epidemiology, King’s College London, London, U.K
| | - Heather M. Stringham
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Joseph Trakalo
- High-Throughput Genomics, Oxford Genomics Centre, Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, U.K
| | - Eric Banks
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
| | - Jason Carey
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
| | | | - Mark DePristo
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
| | - Yossi Farjoun
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
| | - Timothy Fennell
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
| | - Jacqueline I. Goldstein
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - George Grant
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
| | - Martin Hrabé de Angelis
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Institute of Experimental Genetics, School of Life Science Weihenstephan, Technische Universität München, Freising, Germany
| | - Jared Maguire
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
| | - Benjamin M. Neale
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Ryan Poplin
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
| | - Shaun Purcell
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- Center for Human Genetic Research, Department of Medicine, Massachusetts General Hospital, Boston, MA
- Department of Psychiatry, Icahn Institute for Genomics & Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Thomas Schwarzmayr
- Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Khalid Shakir
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
| | - Joshua D. Smith
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA
| | - Tim M. Strom
- Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Human Genetics, Technische Universität München, Neuherberg, Germany
| | - Thomas Wieland
- Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Jaana Lindstrom
- Diabetes Prevention Unit, National Institute for Health and Welfare, Helsinki, Finland
| | - Ivan Brandslund
- Department of Regional Health Research, University of Southern Denmark, Odense, Denmark
- Department of Clinical Biochemistry, Vejle Hospital, Vejle, Denmark
| | - Cramer Christensen
- Department of Internal Medicine and Endocrinology, Vejle Hospital, Vejle, Denmark
| | | | - Timo A. Lakka
- Department of Physiology, Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
- Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
- Department of Clinical Physiology and Nuclear Medicine, Kuopio University Hospital, Kuopio, Finland
| | - Alex S.F. Doney
- Division of Cardiovascular & Diabetes Medicine, Medical Research Institute, Ninewells Hospital and Medical School, Dundee, U.K
| | - Peter Nilsson
- Department of Clinical Sciences, Faculty of Medicine, Lund University, Malmö, Sweden
| | - Nicholas J. Wareham
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, U.K
| | - Claudia Langenberg
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, U.K
| | - Tibor V. Varga
- Department of Clinical Sciences, Lund University Diabetes Centre, and Genetic and Molecular Epidemiology Unit, Lund University, Malmö, Sweden
| | - Paul W. Franks
- Department of Clinical Sciences, Lund University Diabetes Centre, and Genetic and Molecular Epidemiology Unit, Lund University, Malmö, Sweden
- Department of Nutrition, Harvard School of Public Health, Boston, MA
- Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
| | - Olov Rolandsson
- Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
| | - Anders H. Rosengren
- Diabetes and Endocrinology Unit, Department of Clinical Sciences Malmö, Lund University Diabetes Centre, Malmö, Sweden
| | - Vidya S. Farook
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX
| | - Farook Thameem
- Department of Medicine, The University of Texas Health Science Center, San Antonio, TX
| | - Sobha Puppala
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX
| | - Satish Kumar
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX
| | - Donna M. Lehman
- Department of Medicine, The University of Texas Health Science Center, San Antonio, TX
| | - Christopher P. Jenkinson
- Department of Medicine, The University of Texas Health Science Center, San Antonio, TX
- Research and Development Service, South Texas Veterans Health Care System, San Antonio, TX
| | - Joanne E. Curran
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX
| | - Daniel Esten Hale
- Department of Pediatrics, The University of Texas Health Science Center, San Antonio, TX
| | - Sharon P. Fowler
- Department of Medicine, The University of Texas Health Science Center, San Antonio, TX
| | - Rector Arya
- Department of Pediatrics, The University of Texas Health Science Center, San Antonio, TX
| | - Ralph A. DeFronzo
- Department of Medicine, The University of Texas Health Science Center, San Antonio, TX
| | - Hanna E. Abboud
- Department of Medicine, The University of Texas Health Science Center, San Antonio, TX
| | - Ann-Christine Syvänen
- Molecular Medicine and Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Pamela J. Hicks
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC
- Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, NC
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC
| | - Nicholette D. Palmer
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC
- Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, NC
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC
| | - Maggie C.Y. Ng
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC
- Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, NC
| | - Donald W. Bowden
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC
- Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, NC
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC
| | - Barry I. Freedman
- Section on Nephrology, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC
| | - Tõnu Esko
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- Department of Genetics, Harvard Medical School, Boston, MA
- Division of Endocrinology, Boston Children's Hospital, Boston, MA
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Reedik Mägi
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Lili Milani
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | | | | | - Narisu Narisu
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Leena Kinnunen
- Department of Health, National Institute for Health and Welfare, Helsinki, Finland
| | - Lori L. Bonnycastle
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Amy Swift
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Dorota Pasko
- Genetics of Complex Traits, University of Exeter Medical School, Exeter, U.K
| | - Andrew R. Wood
- Genetics of Complex Traits, University of Exeter Medical School, Exeter, U.K
| | - João Fadista
- Diabetes and Endocrinology Unit, Department of Clinical Sciences Malmö, Lund University Diabetes Centre, Malmö, Sweden
| | - Toni I. Pollin
- Program in Personalized and Genomic Medicine, Department of Medicine, University of Maryland, Baltimore, MD
| | - Nir Barzilai
- Departments of Medicine and Genetics, Albert Einstein College of Medicine, New York, NY
| | - Gil Atzmon
- Departments of Medicine and Genetics, Albert Einstein College of Medicine, New York, NY
- Faculty of Natural Sciences, University of Haifa, Haifa, Israel
| | - Benjamin Glaser
- Endocrinology and Metabolism Service, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Barbara Thorand
- German Center for Diabetes Research (DZD), 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
- Department of Genetic Epidemiology, Institute of Medical Informatics, Biometry and Epidemiology, Ludwig-Maximilians-Universität, Munich, Germany
| | - Annette Peters
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Deutsches Zentrum für Herz-Kreislauf-Forschung (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Michael Roden
- Institute of Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University, Düsseldorf, Germany
- German Center for Diabetes Research, Partner Düsseldorf, Germany
| | - Martina Müller-Nurasyid
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Department of Genetic Epidemiology, Institute of Medical Informatics, Biometry and Epidemiology, Ludwig-Maximilians-Universität, Munich, Germany
- Deutsches Zentrum für Herz-Kreislauf-Forschung (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
- Department of Medicine I, University Hospital Grosshadern, Ludwig-Maximilians-Universität, Munich, Germany
| | - Liming Liang
- Department of Epidemiology, Harvard School of Public Health, Boston, MA
- Department of Biostatistics, Harvard School of Public Health, Boston, MA
| | - Jennifer Kriebel
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Thomas Illig
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Hannover Unified Biobank, Hannover Medical School, Hannover, Germany
- Institute of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Harald Grallert
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Christian Gieger
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Christa Meisinger
- Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Lars Lannfelt
- Geriatrics, Department of Public Health and Caring Sciences, Uppsala University, Uppsala, Sweden
| | - Solomon K. Musani
- Jackson Heart Study, University of Mississippi Medical Center, Jackson, MS
| | - Michael Griswold
- Center of Biostatistics and Bioinformatics, University of Mississippi Medical Center, Jackson, MS
| | - Herman A. Taylor
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS
| | - Gregory Wilson
- College of Public Services, Jackson State University, Jackson, MS
| | - Adolfo Correa
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS
| | - Heikki Oksa
- Pirkanmaa Hospital District, Tampere, Finland
| | - William R. Scott
- Department of Epidemiology and Biostatistics, Imperial College London, London, U.K
| | - Uzma Afzal
- Department of Epidemiology and Biostatistics, Imperial College London, London, U.K
| | - Sian-Tsung Tan
- Cardiovascular Sciences, National Heart and Lung Institute, Imperial College London, London, U.K
- Department of Cardiology, Ealing Hospital NHS Trust, Southall, U.K
| | - Marie Loh
- Department of Epidemiology and Biostatistics, Imperial College London, London, U.K
- Institute of Health Sciences, University of Oulu, Oulu, Finland
- Translational Laboratory in Genetic Medicine, Agency for Science, Technology and Research (A*STAR), Singapore
| | - John C. Chambers
- Department of Epidemiology and Biostatistics, Imperial College London, London, U.K
- Department of Cardiology, Ealing Hospital NHS Trust, Southall, U.K
- Imperial College Healthcare NHS Trust, Imperial College London, London, U.K
| | - Jobanpreet Sehmi
- Cardiovascular Sciences, National Heart and Lung Institute, Imperial College London, London, U.K
- Department of Cardiology, Ealing Hospital NHS Trust, Southall, U.K
| | - Jaspal Singh Kooner
- Cardiovascular Sciences, National Heart and Lung Institute, Imperial College London, London, U.K
| | - Benjamin Lehne
- Department of Epidemiology and Biostatistics, Imperial College London, London, U.K
| | - Yoon Shin Cho
- Department of Biomedical Science, Hallym University, Chuncheon, Republic of Korea
| | - Jong-Young Lee
- Ministry of Health and Welfare, Seoul, Republic of Korea
| | - Bok-Ghee Han
- Center for Genome Science, Korea National Research Institute of Health, Chungcheongbuk-do, Republic of Korea
| | - Annemari Käräjämäki
- Vaasa Health Care Center, Vaasa, Finland
- Department of Primary Health Care, Vaasa Central Hospital, Vaasa, Finland
| | - Qibin Qi
- Department of Nutrition, Harvard School of Public Health, Boston, MA
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, New York, NY
| | - Lu Qi
- Department of Nutrition, Harvard 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
| | - Jinyan Huang
- Department of Epidemiology, Harvard School of Public Health, Boston, MA
| | - Frank B. Hu
- Department of Nutrition, Harvard School of Public Health, Boston, MA
- Department of Epidemiology, Harvard School of Public Health, Boston, MA
| | - Olle Melander
- Hypertension and Cardiovascular Disease, Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - Marju Orho-Melander
- Diabetes and Cardiovascular Disease–Genetic Epidemiology, Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - Jennifer E. Below
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX
| | - David Aguilar
- Cardiovascular Division, Baylor College of Medicine, Houston, TX
| | - Tien Yin Wong
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Jianjun Liu
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
- Division of Human Genetics, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Chiea-Chuen Khor
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Division of Human Genetics, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Kee Seng Chia
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Wei Yen Lim
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Ching-Yu Cheng
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Office of Clinical Sciences, Centre for Quantitative Medicine, Duke-NUS Graduate Medical School Singapore, Singapore
| | - Edmund Chan
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - E Shyong Tai
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Graduate Medical School Singapore, Singapore
| | - Tin Aung
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Allan Linneberg
- Research Centre for Prevention and Health, Glostrup University Hospital, Glostrup, Denmark
- Department of Clinical Experimental Research, Rigshospitalet, Glostrup, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Bo Isomaa
- Folkhälsan Research Center, Helsinki, Finland
- Department of Social Services and Health Care, Jakobstad, Finland
| | - Thomas Meitinger
- Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Human Genetics, Technische Universität München, Neuherberg, Germany
- Deutsches Zentrum für Herz-Kreislauf-Forschung (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Tiinamaija Tuomi
- Folkhälsan Research Center, Helsinki, Finland
- Department of Endocrinology, Helsinki University Central Hospital, Helsinki, Finland
| | | | - Jasmina Kravic
- Diabetes and Endocrinology Unit, Department of Clinical Sciences Malmö, Lund University Diabetes Centre, Malmö, Sweden
| | | | - Torsten Lauritzen
- Section of General Practice, Department of Public Health, Aarhus University, Aarhus, Denmark
| | - Panos Deloukas
- Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton, U.K
| | - Kathleen E. Stirrups
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, U.K
- Department of Haematology, University of Cambridge, Cambridge, U.K
| | - Katharine R. Owen
- Oxford Centre for Diabetes, Endocrinology & Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, U.K
- Oxford NIHR Biomedical Research Centre, Oxford University Hospitals Trust, Oxford, U.K
| | - Andrew J. Farmer
- Department of Primary Care Health Sciences, University of Oxford, Oxford, U.K
| | - Timothy M. Frayling
- Genetics of Complex Traits, University of Exeter Medical School, Exeter, U.K
| | - Stephen P. O'Rahilly
- Metabolic Research Laboratories, Institute of Metabolic Science, University of Cambridge, Cambridge, U.K
| | - Mark Walker
- Institute of Cellular Medicine, University of Newcastle, Newcastle, U.K
| | - Jonathan C. Levy
- Oxford Centre for Diabetes, Endocrinology & Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, U.K
| | - Dylan Hodgkiss
- Department of Twin Research & Genetic Epidemiology, King’s College London, London, U.K
| | | | - Teemu Kuulasmaa
- Internal Medicine, Institute of Clinical Medicine, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
| | - Alena Stančáková
- Internal Medicine, Institute of Clinical Medicine, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
| | - Inês Barroso
- Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton, U.K
- Metabolic Research Laboratories, Institute of Metabolic Science, University of Cambridge, Cambridge, U.K
| | - Dwaipayan Bharadwaj
- Functional Genomics Unit, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India
| | - Juliana Chan
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Hong Kong, China
| | | | - Mark J. Daly
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Peter J. Donnelly
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, U.K
- Department of Statistics, University of Oxford, Oxford, U.K
| | | | - Paul Elliott
- Department of Epidemiology and Biostatistics, Imperial College London, London, U.K
- MRC-PHE Centre for Environment & Health, Imperial College London, London, U.K
| | - Tasha Fingerlin
- Department of Epidemiology, Colorado School of Public Health, University of Colorado, Aurora, CO
| | - Philippe Froguel
- Genomics and Molecular Physiology, CNRS Institut de Biologie de Lille, Lille, France
| | - Cheng Hu
- Department of Endocrinology and Metabolism, Shanghai Diabetes Institute, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Weiping Jia
- Department of Endocrinology and Metabolism, Shanghai Diabetes Institute, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Ronald C.W. Ma
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Hong Kong, China
| | - Gilean McVean
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, U.K
| | - Taesung Park
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
- Department of Statistics, Seoul National University, Seoul, Republic of Korea
| | | | - Manjinder Sandhu
- Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton, U.K
- Institute of Public Health, Department of Public Health and Primary Care, University of Cambridge, Cambridge, U.K
| | - James Scott
- Cardiovascular Sciences, National Heart and Lung Institute, Imperial College London, London, U.K
| | - Rob Sladek
- McGill University and Génome Québec Innovation Centre, Montreal, Canada
- Department of Human Genetics, McGill University, Montreal, Canada
- Division of Endocrinology and Metabolism, Department of Medicine, McGill University, Montreal, Canada
| | - Nikhil Tandon
- Department of Endocrinology and Metabolism, All India Institute of Medical Sciences, New Delhi, India
| | - Yik Ying Teo
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
- Life Sciences Institute, National University of Singapore, Singapore
- Department of Statistics and Applied Probability, National University of Singapore, Singapore
| | - Eleftheria Zeggini
- Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton, U.K
| | - Richard M. Watanabe
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA
- Department of Physiology and Biophysics, Keck School of Medicine, University of Southern California, Los Angeles, CA
- Diabetes & Obesity Research Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Heikki A. Koistinen
- Department of Health, National Institute for Health and Welfare, Helsinki, Finland
- Department of Medicine and Abdominal Center, Endocrinology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | - Y. Antero Kesaniemi
- Institute of Clinical Medicine, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Matti Uusitupa
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Timothy D. Spector
- Department of Twin Research & Genetic Epidemiology, King’s College London, London, U.K
| | - Veikko Salomaa
- Department of Health, National Institute for Health and Welfare, Helsinki, Finland
| | - Rainer Rauramaa
- Foundation for Research in Health Exercise and Nutrition, Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
| | - Colin N.A. Palmer
- Pat Macpherson Centre for Pharmacogenetics and Pharmacogenomics, Medical Research Institute, Ninewells Hospital and Medical School, Dundee, U.K
| | - Inga Prokopenko
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, U.K
- Oxford Centre for Diabetes, Endocrinology & Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, U.K
- Department of Genomics of Common Disease, School of Public Health, Imperial College London, London, U.K
| | - Andrew D. Morris
- Division for Molecular Medicine, Clinical Research Centre, Ninewells Hospital and Medical School, Dundee, U.K
| | - 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
| | - Lars Lind
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Erik Ingelsson
- Molecular Medicine and Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA
| | - Jaakko Tuomilehto
- Diabetes Prevention Unit, National Institute for Health and Welfare, Helsinki, Finland
- Center for Vascular Prevention, Danube University Krems, Krems, Austria
- Diabetes Research Group, King Abdulaziz University, Jeddah, Saudi Arabia
- Dasman Diabetes Institute, Dasman, Kuwait
| | - Fredrik Karpe
- Oxford Centre for Diabetes, Endocrinology & Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, U.K
- Oxford NIHR Biomedical Research Centre, Oxford University Hospitals Trust, Oxford, U.K
| | - Leif Groop
- Diabetes and Endocrinology Unit, Department of Clinical Sciences Malmö, Lund University Diabetes Centre, Malmö, Sweden
| | - Torben Jørgensen
- Research Centre for Prevention and Health, Glostrup University Hospital, Glostrup, Denmark
- Faculty of Medicine, University of Aalborg, Aalborg, Denmark
| | - Torben Hansen
- The 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
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Johanna Kuusisto
- Internal Medicine, Institute of Clinical Medicine, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
- Kuopio University Hospital, Kuopio, Finland
| | - Gonçalo Abecasis
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Graeme I. Bell
- Departments of Medicine and Human Genetics, The University of Chicago, Chicago, IL
| | - John Blangero
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX
| | - Nancy J. Cox
- Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL
| | | | - Mark Seielstad
- Department of Laboratory Medicine, Institute for Human Genetics, University of California, San Francisco, San Francisco, CA
- Blood Systems Research Institute, San Francisco, CA
| | - James G. Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS
| | - Josee Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
- Framingham Heart Study, National Heart, Lung, and Blood Institute, Framingham, MA
| | - Samuli Ripatti
- Wellcome Trust Sanger Institute, Hinxton, U.K
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- Hjelt Institute, University of Helsinki, Helsinki, Finland
| | - Craig L. Hanis
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX
| | - Jose C. Florez
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- Center for Human Genetic Research, Department of Medicine, Massachusetts General Hospital, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
- Diabetes Research Center (Diabetes Unit), Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Karen L. Mohlke
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - James B. Meigs
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- Department of Medicine, Harvard Medical School, Boston, MA
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA
| | - Markku Laakso
- Internal Medicine, Institute of Clinical Medicine, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
- Kuopio University Hospital, Kuopio, Finland
| | - Andrew P. Morris
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, U.K
- Estonian Genome Center, University of Tartu, Tartu, Estonia
- Department of Biostatistics, University of Liverpool, Liverpool, U.K
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - David Altshuler
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- Department of Medicine, Harvard Medical School, Boston, MA
- Department of Genetics, Harvard Medical School, Boston, MA
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA
- Diabetes Research Center (Diabetes Unit), Department of Medicine, Massachusetts General Hospital, Boston, MA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA
| | - Mark I. McCarthy
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, U.K
- Oxford Centre for Diabetes, Endocrinology & Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, U.K
- Oxford NIHR Biomedical Research Centre, Oxford University Hospitals Trust, Oxford, U.K
| | - Anna L. Gloyn
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, U.K
- Oxford Centre for Diabetes, Endocrinology & Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, U.K
- Oxford NIHR Biomedical Research Centre, Oxford University Hospitals Trust, Oxford, U.K
| | - Cecilia M. Lindgren
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, U.K
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, U.K
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Abstract
High-throughput technologies have revolutionized medical research. The advent of genotyping arrays enabled large-scale genome-wide association studies and methods for examining global transcript levels, which gave rise to the field of “integrative genetics”. Other omics technologies, such as proteomics and metabolomics, are now often incorporated into the everyday methodology of biological researchers. In this review, we provide an overview of such omics technologies and focus on methods for their integration across multiple omics layers. As compared to studies of a single omics type, multi-omics offers the opportunity to understand the flow of information that underlies disease.
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Affiliation(s)
- Yehudit Hasin
- Department of Medicine, University of California, 10833 Le Conte Avenue, A2-237 CHS, Los Angeles, CA, 90095, USA.,Department of Human Genetics, University of California, 10833 Le Conte Avenue, A2-237 CHS, Los Angeles, CA, 90095, USA
| | - Marcus Seldin
- Department of Medicine, University of California, 10833 Le Conte Avenue, A2-237 CHS, Los Angeles, CA, 90095, USA
| | - Aldons Lusis
- Department of Medicine, University of California, 10833 Le Conte Avenue, A2-237 CHS, Los Angeles, CA, 90095, USA. .,Department of Microbiology, Immunology and Molecular Genetics, 10833 Le Conte Avenue, A2-237 CHS, Los Angeles, CA, 90095, USA. .,Department of Human Genetics, University of California, 10833 Le Conte Avenue, A2-237 CHS, Los Angeles, CA, 90095, USA.
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Laakso M, Kuusisto J, Stančáková A, Kuulasmaa T, Pajukanta P, Lusis AJ, Collins FS, Mohlke KL, Boehnke M. The Metabolic Syndrome in Men study: a resource for studies of metabolic and cardiovascular diseases. J Lipid Res 2017; 58:481-493. [PMID: 28119442 DOI: 10.1194/jlr.o072629] [Citation(s) in RCA: 130] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 01/15/2017] [Indexed: 12/30/2022] Open
Abstract
The Metabolic Syndrome in Men (METSIM) study is a population-based study including 10,197 Finnish men examined in 2005-2010. The aim of the study is to investigate nongenetic and genetic factors associated with the risk of T2D and CVD, and with cardiovascular risk factors. The protocol includes a detailed phenotyping of the participants, an oral glucose tolerance test, fasting laboratory measurements including proton NMR measurements, mass spectometry metabolomics, adipose tissue biopsies from 1,400 participants, and a stool sample. In our ongoing follow-up study, we have, to date, reexamined 6,496 participants. Extensive genotyping and exome sequencing have been performed for essentially all METSIM participants, and >2,000 METSIM participants have been whole-genome sequenced. We have identified several nongenetic markers associated with the development of diabetes and cardiovascular events, and participated in several genetic association studies to identify gene variants associated with diabetes, hyperglycemia, and cardiovascular risk factors. The generation of a phenotype and genotype resource in the METSIM study allows us to proceed toward a "systems genetics" approach, which includes statistical methods to quantitate and integrate intermediate phenotypes, such as transcript, protein, or metabolite levels, to provide a global view of the molecular architecture of complex traits.
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Affiliation(s)
- Markku Laakso
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland .,Department of Medicine, Kuopio University Hospital, Kuopio, Finland
| | - Johanna Kuusisto
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland.,Department of Medicine, Kuopio University Hospital, Kuopio, Finland
| | - Alena Stančáková
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland
| | - Teemu Kuulasmaa
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland
| | - Päivi Pajukanta
- Departments of Human Genetics David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA
| | - Aldons J Lusis
- Departments of Human Genetics David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA.,Medicine, David Geffen School of Medicine at University of California, Los Angeles, 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
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI
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