1
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Costanzo MC, von Grotthuss M, Massung J, Jang D, Caulkins L, Koesterer R, Gilbert C, Welch RP, Kudtarkar P, Hoang Q, Boughton AP, Singh P, Sun Y, Duby M, Moriondo A, Nguyen T, Smadbeck P, Alexander BR, Brandes M, Carmichael M, Dornbos P, Green T, Huellas-Bruskiewicz KC, Ji Y, Kluge A, McMahon AC, Mercader JM, Ruebenacker O, Sengupta S, Spalding D, Taliun D, Smith P, Thomas MK, Akolkar B, Brosnan MJ, Cherkas A, Chu AY, Fauman EB, Fox CS, Kamphaus TN, Miller MR, Nguyen L, Parsa A, Reilly DF, Ruetten H, Wholley D, Zaghloul NA, Abecasis GR, Altshuler D, Keane TM, McCarthy MI, Gaulton KJ, Florez JC, Boehnke M, Burtt NP, Flannick J. The Type 2 Diabetes Knowledge Portal: An open access genetic resource dedicated to type 2 diabetes and related traits. Cell Metab 2023; 35:695-710.e6. [PMID: 36963395 PMCID: PMC10231654 DOI: 10.1016/j.cmet.2023.03.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 10/23/2022] [Accepted: 02/28/2023] [Indexed: 03/26/2023]
Abstract
Associations between human genetic variation and clinical phenotypes have become a foundation of biomedical research. Most repositories of these data seek to be disease-agnostic and therefore lack disease-focused views. The Type 2 Diabetes Knowledge Portal (T2DKP) is a public resource of genetic datasets and genomic annotations dedicated to type 2 diabetes (T2D) and related traits. Here, we seek to make the T2DKP more accessible to prospective users and more useful to existing users. First, we evaluate the T2DKP's comprehensiveness by comparing its datasets with those of other repositories. Second, we describe how researchers unfamiliar with human genetic data can begin using and correctly interpreting them via the T2DKP. Third, we describe how existing users can extend their current workflows to use the full suite of tools offered by the T2DKP. We finally discuss the lessons offered by the T2DKP toward the goal of democratizing access to complex disease genetic results.
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Affiliation(s)
- Maria C Costanzo
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA
| | - Marcin von Grotthuss
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA
| | - Jeffrey Massung
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA
| | - Dongkeun Jang
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA
| | - Lizz Caulkins
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA
| | - Ryan Koesterer
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA
| | - Clint Gilbert
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA
| | - Ryan P Welch
- Department of Biostatistics and The Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Parul Kudtarkar
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92161, USA
| | - Quy Hoang
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA
| | - Andrew P Boughton
- Department of Biostatistics and The Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Preeti Singh
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA
| | - Ying Sun
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92161, USA
| | - Marc Duby
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA
| | - Annie Moriondo
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA
| | - Trang Nguyen
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA
| | - Patrick Smadbeck
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA
| | - Benjamin R Alexander
- Simulation and Modeling Sciences, Pfizer Worldwide Research, Development and Medical, Cambridge, MA 02139, USA
| | - MacKenzie Brandes
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA
| | - Mary Carmichael
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA
| | - Peter Dornbos
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA; Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Todd Green
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA
| | - Kenneth C Huellas-Bruskiewicz
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA
| | - Yue Ji
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Alexandria Kluge
- Genomics Platform, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA
| | - Aoife C McMahon
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Josep M Mercader
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Oliver Ruebenacker
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA
| | - Sebanti Sengupta
- Department of Biostatistics and The Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Dylan Spalding
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Daniel Taliun
- Department of Biostatistics and The Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Philip Smith
- National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA
| | - Melissa K Thomas
- Tailored Therapeutics-Diabetes, Eli Lilly and Company, Lilly Corporate Center DC 0545, Indianapolis, IN 46285, USA
| | - Beena Akolkar
- National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA
| | - M Julia Brosnan
- Internal Medicine Research Unit, Pfizer Worldwide Research, Development and Medical, Cambridge, MA 02139, USA
| | - Andriy Cherkas
- Team Early Projects Type 1 Diabetes, Therapeutic Area Diabetes and Cardiovascular Medicine, Research & Development, Sanofi, Industriepark Höchst-H831, Frankfurt am Main 65926, Germany
| | - Audrey Y Chu
- Merck Research Laboratories, Boston, MA 02115, USA
| | - Eric B Fauman
- Integrative Biology, Internal Medicine Research Unit, Pfizer Worldwide Research, Development and Medical, Cambridge, MA 02139, USA
| | | | | | - Melissa R Miller
- Internal Medicine Research Unit, Pfizer Worldwide Research, Development and Medical, Cambridge, MA 02139, USA
| | - Lynette Nguyen
- Foundation for the National Institutes of Health, North Bethesda, MD 20852, USA
| | - Afshin Parsa
- National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA
| | | | - Hartmut Ruetten
- CardioMetabolism & Respiratory Medicine, Boehringer Ingelheim International GmbH, 55216 Ingelheim/Rhein, Germany
| | - David Wholley
- Foundation for the National Institutes of Health, North Bethesda, MD 20852, USA
| | - Norann A Zaghloul
- National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA
| | - Gonçalo R Abecasis
- Department of Biostatistics and The Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA; Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | - David Altshuler
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA
| | - Thomas M Keane
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Mark I McCarthy
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 9DU, UK; Oxford Centre for Diabetes Endocrinology & Metabolism, University of Oxford, Oxford OX3 7BN, UK
| | - Kyle J Gaulton
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92161, USA
| | - Jose C Florez
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Michael Boehnke
- Department of Biostatistics and The Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Noël P Burtt
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA.
| | - Jason Flannick
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA; Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA.
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Boughton AP, Welch RP, Flickinger M, VandeHaar P, Taliun D, Abecasis GR, Boehnke M. LocusZoom.js: interactive and embeddable visualization of genetic association study results. Bioinformatics 2021; 37:3017-3018. [PMID: 33734315 PMCID: PMC8479674 DOI: 10.1093/bioinformatics/btab186] [Citation(s) in RCA: 115] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 02/25/2021] [Accepted: 03/16/2021] [Indexed: 02/02/2023] Open
Abstract
SUMMARY LocusZoom.js is a JavaScript library for creating interactive web-based visualizations of genetic association study results. It can display one or more traits in the context of relevant biological data (such as gene models and other genomic annotation), and allows interactive refinement of analysis models (by selecting linkage disequilibrium reference panels, identifying sets of likely causal variants, or comparisons to the GWAS catalog). It can be embedded in web pages to enable data sharing and exploration. Views can be customized and extended to display other data types such as phenome-wide association study (PheWAS) results, chromatin co-accessibility, or eQTL measurements. A new web upload service harmonizes datasets, adds annotations, and makes it easy to explore user-provided result sets. AVAILABILITY AND IMPLEMENTATION LocusZoom.js is open-source software under a permissive MIT license. Code and documentation are available at: https://github.com/statgen/locuszoom/. Installable packages for all versions are also distributed via NPM. Additional features are provided as standalone libraries to promote reuse. Use with your own GWAS results at https://my.locuszoom.org/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Andrew P Boughton
- Department of Biostatistics and the Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ryan P Welch
- Department of Biostatistics and the Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Matthew Flickinger
- Department of Biostatistics and the Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Peter VandeHaar
- Department of Biostatistics and the Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Daniel Taliun
- Department of Biostatistics and the Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Gonçalo R Abecasis
- Department of Biostatistics and the Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA,Present address: Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | - Michael Boehnke
- Department of Biostatistics and the Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA,To whom correspondence should be addressed.
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3
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Gagliano Taliun SA, VandeHaar P, Boughton AP, Welch RP, Taliun D, Schmidt EM, Zhou W, Nielsen JB, Willer CJ, Lee S, Fritsche LG, Boehnke M, Abecasis GR. Exploring and visualizing large-scale genetic associations by using PheWeb. Nat Genet 2020; 52:550-552. [PMID: 32504056 DOI: 10.1038/s41588-020-0622-5] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Sarah A Gagliano Taliun
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA.,Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Peter VandeHaar
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA.,Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Andrew P Boughton
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA.,Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Ryan P Welch
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA.,Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Daniel Taliun
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA.,Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Ellen M Schmidt
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA.,Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Wei Zhou
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Jonas B Nielsen
- Department of Internal Medicine, Division of Cardiology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Cristen J Willer
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.,Department of Internal Medicine, Division of Cardiology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Seunggeun Lee
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA.,Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Lars G Fritsche
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA.,Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Michael Boehnke
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA.,Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Gonçalo R Abecasis
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA. .,Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA. .,Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, NY, USA.
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4
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Flannick J, Mercader JM, Fuchsberger C, Udler MS, Mahajan A, Wessel J, Teslovich TM, Caulkins L, Koesterer R, Barajas-Olmos F, Blackwell TW, Boerwinkle E, Brody JA, Centeno-Cruz F, Chen L, Chen S, Contreras-Cubas C, Córdova E, Correa A, Cortes M, DeFronzo RA, Dolan L, Drews KL, Elliott A, Floyd JS, Gabriel S, Garay-Sevilla ME, García-Ortiz H, Gross M, Han S, Heard-Costa NL, Jackson AU, Jørgensen ME, Kang HM, Kelsey M, Kim BJ, Koistinen HA, Kuusisto J, Leader JB, Linneberg A, Liu CT, Liu J, Lyssenko V, Manning AK, Marcketta A, Malacara-Hernandez JM, Martínez-Hernández A, Matsuo K, Mayer-Davis E, Mendoza-Caamal E, Mohlke KL, Morrison AC, Ndungu A, Ng MCY, O'Dushlaine C, Payne AJ, Pihoker C, Post WS, Preuss M, Psaty BM, Vasan RS, Rayner NW, Reiner AP, Revilla-Monsalve C, Robertson NR, Santoro N, Schurmann C, So WY, Soberón X, Stringham HM, Strom TM, Tam CHT, Thameem F, Tomlinson B, Torres JM, Tracy RP, van Dam RM, Vujkovic M, Wang S, Welch RP, Witte DR, Wong TY, Atzmon G, Barzilai N, Blangero J, Bonnycastle LL, Bowden DW, Chambers JC, Chan E, Cheng CY, Cho YS, Collins FS, de Vries PS, Duggirala R, Glaser B, Gonzalez C, Gonzalez ME, Groop L, Kooner JS, Kwak SH, Laakso M, Lehman DM, Nilsson P, Spector TD, Tai ES, Tuomi T, Tuomilehto J, Wilson JG, Aguilar-Salinas CA, Bottinger E, Burke B, Carey DJ, Chan JCN, Dupuis J, Frossard P, Heckbert SR, Hwang MY, Kim YJ, Kirchner HL, Lee JY, Lee J, Loos RJF, Ma RCW, Morris AD, O'Donnell CJ, Palmer CNA, Pankow J, Park KS, Rasheed A, Saleheen D, Sim X, Small KS, Teo YY, Haiman C, Hanis CL, Henderson BE, Orozco L, Tusié-Luna T, Dewey FE, Baras A, Gieger C, Meitinger T, Strauch K, Lange L, Grarup N, Hansen T, Pedersen O, Zeitler P, Dabelea D, Abecasis G, Bell GI, Cox NJ, Seielstad M, Sladek R, Meigs JB, Rich SS, Rotter JI, Altshuler D, Burtt NP, Scott LJ, Morris AP, Florez JC, McCarthy MI, Boehnke M. Exome sequencing of 20,791 cases of type 2 diabetes and 24,440 controls. Nature 2019; 570:71-76. [PMID: 31118516 PMCID: PMC6699738 DOI: 10.1038/s41586-019-1231-2] [Citation(s) in RCA: 186] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 04/23/2019] [Indexed: 02/08/2023]
Abstract
Protein-coding genetic variants that strongly affect disease risk can yield relevant clues to disease pathogenesis. Here we report exome-sequencing analyses of 20,791 individuals with type 2 diabetes (T2D) and 24,440 non-diabetic control participants from 5 ancestries. We identify gene-level associations of rare variants (with minor allele frequencies of less than 0.5%) in 4 genes at exome-wide significance, including a series of more than 30 SLC30A8 alleles that conveys protection against T2D, and in 12 gene sets, including those corresponding to T2D drug targets (P = 6.1 × 10-3) and candidate genes from knockout mice (P = 5.2 × 10-3). Within our study, the strongest T2D gene-level signals for rare variants explain at most 25% of the heritability of the strongest common single-variant signals, and the gene-level effect sizes of the rare variants that we observed in established T2D drug targets will require 75,000-185,000 sequenced cases to achieve exome-wide significance. We propose a method to interpret these modest rare-variant associations and to incorporate these associations into future target or gene prioritization efforts.
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Affiliation(s)
- Jason Flannick
- Program in Metabolism, Broad Institute, Cambridge, MA, USA.
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
- Program in Medical & Population Genetics, Broad Institute, Cambridge, MA, USA.
| | - Josep M Mercader
- Program in Metabolism, Broad Institute, Cambridge, MA, USA
- Program in Medical & Population Genetics, Broad Institute, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Diabetes Research Center (Diabetes Unit), Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Christian Fuchsberger
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
- Institute for Biomedicine, Eurac Research, Bolzano, Italy
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Miriam S Udler
- Program in Metabolism, Broad Institute, Cambridge, MA, USA
- Program in Medical & Population Genetics, Broad Institute, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Diabetes Research Center (Diabetes Unit), Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Anubha Mahajan
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Jennifer Wessel
- Department of Epidemiology, Fairbanks School of Public Health, Indiana University, Indianapolis, IN, USA
- Department of Medicine, School of Medicine, Indiana University, Indianapolis, IN, USA
- Diabetes Translational Research Center, Indiana University, Indianapolis, IN, USA
| | - Tanya M Teslovich
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Lizz Caulkins
- Program in Metabolism, Broad Institute, Cambridge, MA, USA
- Program in Medical & Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Ryan Koesterer
- Program in Metabolism, Broad Institute, Cambridge, MA, USA
- Program in Medical & Population Genetics, Broad Institute, Cambridge, MA, USA
| | | | - Thomas W Blackwell
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Jennifer A Brody
- Cardiovascular Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | | | - Ling Chen
- Diabetes Research Center (Diabetes Unit), Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Siying Chen
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | | | - Emilio Córdova
- Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Adolfo Correa
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Maria Cortes
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ralph A DeFronzo
- Department of Medicine, University of Texas Health Science Center, San Antonio, TX, USA
| | - Lawrence Dolan
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Kimberly L Drews
- Biostatistics Center, George Washington University, Rockville, MD, USA
| | - Amanda Elliott
- Program in Metabolism, Broad Institute, Cambridge, MA, USA
- Program in Medical & Population Genetics, Broad Institute, Cambridge, MA, USA
- Diabetes Research Center (Diabetes Unit), Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - James S Floyd
- Department of Medicine and Epidemiology, University of Washington, Seattle, WA, USA
| | | | - Maria Eugenia Garay-Sevilla
- Department of Medicine, The University of Chicago, Chicago, IL, USA
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA
| | | | - Myron Gross
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Sohee Han
- Division of Genome Research, Center for Genome Science, National Institute of Health, Chungcheongbuk-do, South Korea
| | - Nancy L Heard-Costa
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
- National Heart Lung and Blood Institute's Framingham Heart Study, Framingham, MA, USA
| | - Anne U Jackson
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Marit E Jørgensen
- Steno Diabetes Center Copenhagen, Gentofte, Denmark
- National Institute of Public Health, University of Southern Denmark, Copenhagen, Denmark
- Greenland Centre for Health Research, University of Greenland, Nuuk, Greenland
| | - Hyun Min Kang
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Megan Kelsey
- Biostatistics Center, George Washington University, Rockville, MD, USA
| | - Bong-Jo Kim
- Division of Genome Research, Center for Genome Science, National Institute of Health, Chungcheongbuk-do, South Korea
| | - Heikki A Koistinen
- Department of Public Health Solutions, National Institute for Health and Welfare, Helsinki, Finland
- University of Helsinki and Department of Medicine, Helsinki University Central Hospital, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | - Johanna Kuusisto
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland
- Department of Medicin, Kuopio University Hospital, Kuopio, Finland
| | | | - Allan Linneberg
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Center for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, Copenhagen, Denmark
- Department of Clinical Experimental Research, Rigshospitalet, Copenhagen, Denmark
| | - Ching-Ti Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Jianjun Liu
- 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, National University Health System, Singapore, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Valeriya Lyssenko
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University Diabetes Centre, Malmö, Sweden
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Alisa K Manning
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Harvard University, Boston, MA, USA
| | - Anthony Marcketta
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Juan Manuel Malacara-Hernandez
- Department of Medicine, The University of Chicago, Chicago, IL, USA
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA
| | | | - Karen Matsuo
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | | | | | - Karen L Mohlke
- Department of Genetics, University of North Carolina Chapel Hill, Chapel Hill, NC, USA
| | - Alanna C Morrison
- Human Genetics Center, Department of Epidemiology Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Anne Ndungu
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Maggie C Y Ng
- Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, NC, USA
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC, USA
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Colm O'Dushlaine
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Anthony J Payne
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Wendy S Post
- Division of Cardiology, Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Michael Preuss
- Charles R. Bronfman Institute of Personalized Medicine, Mount Sinai School of Medicine, New York, NY, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Health Services, University of Washington, Seattle, WA, USA
| | - Ramachandran S Vasan
- National Heart Lung and Blood Institute's Framingham Heart Study, Framingham, MA, USA
- Preventive Medicine & Epidemiology, Medicine, Boston University School of Medicine, Boston, MA, USA
| | - N William Rayner
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | | | | | - Neil R Robertson
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Nicola Santoro
- Department of Pediatrics, Yale University, New Haven, CT, USA
| | - Claudia Schurmann
- Charles R. Bronfman Institute of Personalized Medicine, Mount Sinai School of Medicine, New York, NY, USA
| | - Wing Yee So
- 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
| | - Xavier Soberón
- Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Heather M Stringham
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Tim M Strom
- Institute of Human Genetics, Technische Universität München, Munich, Germany
- Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Claudia H T Tam
- 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
| | - Farook Thameem
- Health Science Center, Department of Biochemistry, Faculty of Medicine, Kuwait University, Safat, Kuwait
| | - Brian Tomlinson
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Jason M Torres
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Russell P Tracy
- Department of Pathology and Laboratory Medicine, The Robert Larner M.D. College of Medicine, University of Vermont, Burlington, VT, USA
- Department of Biochemistry, The Robert Larner M.D. College of Medicine, University of Vermont, Burlington, VT, USA
| | - Rob M van Dam
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, Singapore, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
- Department of Nutrition, Harvard School of Public Health, Boston, MA, USA
| | - Marijana Vujkovic
- Department of Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Shuai Wang
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Ryan P Welch
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Daniel R Witte
- Department of Public Health, Aarhus University, Aarhus, Denmark
- Danish Diabetes Academy, Odense, Denmark
| | - 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, National University Health System, Singapore, Singapore
| | - Gil Atzmon
- Department of Medicine, Albert Einstein College of Medicine, New York, NY, USA
- Faculty of Natural Science, University of Haifa, Haifa, Israel
- Department of Genetics, Albert Einstein College of Medicine, New York, NY, USA
| | - Nir Barzilai
- Department of Medicine, Albert Einstein College of Medicine, New York, NY, USA
- Department of Genetics, Albert Einstein College of Medicine, New York, NY, USA
| | - John Blangero
- Department of Human Genetics, University of Texas Rio Grande Valley, Edinburg, TX, USA
- South Texas Diabetes and Obesity Institute, Brownsville, TX, USA
| | - Lori L Bonnycastle
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Donald W Bowden
- Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, NC, USA
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC, USA
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - John C Chambers
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- Department of Cardiology, Ealing Hospital NHS Trust, Southall, UK
- Imperial College Healthcare NHS Trust, Imperial College London, London, UK
| | - Edmund Chan
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, Singapore, Singapore
| | - Ching-Yu Cheng
- Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
| | - Yoon Shin Cho
- Department of Biomedical Science, Hallym University, Chuncheon, South Korea
| | - Francis S Collins
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Paul S de Vries
- Human Genetics Center, Department of Epidemiology Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Ravindranath Duggirala
- Department of Human Genetics, University of Texas Rio Grande Valley, Edinburg, TX, USA
- South Texas Diabetes and Obesity Institute, Brownsville, TX, USA
| | - Benjamin Glaser
- Endocrinology and Metabolism Service, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Clicerio Gonzalez
- Unidad de Diabetes y Riesgo Cardiovascular, Instituto Nacional de Salud Pública, Cuernavaca, Mexico
| | | | - Leif Groop
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University Diabetes Centre, Malmö, Sweden
- Institute for Molecular Genetics Finland, University of Helsinki, Helsinki, Finland
| | - Jaspal Singh Kooner
- National Heart and Lung Institute, Cardiovascular Sciences, Imperial College London, London, UK
| | - Soo Heon Kwak
- Department of Internal Medicine, Seoul National University Hospital, Seoul, South Korea
| | - Markku Laakso
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland
- Department of Medicin, Kuopio University Hospital, Kuopio, Finland
| | - Donna M Lehman
- Department of Medicine, University of Texas Health Science Center, San Antonio, TX, USA
| | - Peter Nilsson
- Department of Clinical Sciences, Medicine, Lund University, Malmö, Sweden
| | - Timothy D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - E Shyong Tai
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, Singapore, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
- Duke-NUS Medical School Singapore, Singapore, Singapore
| | - Tiinamaija Tuomi
- Institute for Molecular Genetics Finland, University of Helsinki, Helsinki, Finland
- Folkhälsan Research Centre, Helsinki, Finland
- Department of Endocrinology, Abdominal Centre, Helsinki University Hospital, Helsinki, Finland
- Research Programs Unit, Diabetes and Obesity, University of Helsinki, Helsinki, Finland
| | - 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
- Instituto de Investigacion Sanitaria del Hospital Universario LaPaz (IdiPAZ), University Hospital LaPaz, Autonomous University of Madrid, Madrid, Spain
| | - James G Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS, USA
| | | | - Erwin Bottinger
- Charles R. Bronfman Institute of Personalized Medicine, Mount Sinai School of Medicine, New York, NY, USA
| | - Brian Burke
- Biostatistics Center, George Washington University, Rockville, MD, USA
| | | | - Juliana C N 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
| | - Josée Dupuis
- National Heart Lung and Blood Institute's Framingham Heart Study, Framingham, MA, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | | | - Susan R Heckbert
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Mi Yeong Hwang
- Division of Genome Research, Center for Genome Science, National Institute of Health, Chungcheongbuk-do, South Korea
| | - Young Jin Kim
- Division of Genome Research, Center for Genome Science, National Institute of Health, Chungcheongbuk-do, South Korea
| | | | - Jong-Young Lee
- Department of Business Data Convergence, Chungbuk National University, Gyeonggi-do, South Korea
| | - Juyoung Lee
- Division of Genome Research, Center for Genome Science, National Institute of Health, Chungcheongbuk-do, South Korea
| | - Ruth J F Loos
- Charles R. Bronfman Institute of Personalized Medicine, Mount Sinai School of Medicine, New York, NY, USA
- The Mindich Child Health and Development Insititute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - 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
| | - Andrew D Morris
- Clinical Research Centre, Centre for Molecular Medicine, Ninewells Hospital and Medical School, Dundee, UK
| | - Christopher J O'Donnell
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Section of Cardiology, Department of Medicine, VA Boston Healthcare, Boston, MA, USA
- Brigham and Women's Hospital, Boston, MA, USA
- Intramural Administration Management Branch, National Heart Lung and Blood Institute, NIH, Framingham, MA, USA
| | - Colin N A Palmer
- Pat Macpherson Centre for Pharmacogenetics and Pharmacogenomics, Medical Research Institute, Ninewells Hospital and Medical School, Dundee, UK
| | - James Pankow
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, MN, USA
| | - Kyong Soo Park
- National Heart and Lung Institute, Cardiovascular Sciences, Imperial College London, London, UK
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, South Korea
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Asif Rasheed
- Center for Non-Communicable Diseases, Karachi, Pakistan
| | - Danish Saleheen
- Department of Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia, PA, USA
- Center for Non-Communicable Diseases, Karachi, Pakistan
| | - Xueling Sim
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Kerrin S Small
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Yik Ying Teo
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
- Life Sciences Institute, National University of Singapore, Singapore, Singapore
- Department of Statistics and Applied Probability, National University of Singapore, Singapore, Singapore
| | - Christopher Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Craig L Hanis
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Brian E Henderson
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Lorena Orozco
- Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Teresa Tusié-Luna
- Instituto Nacional de Ciencias Medicas y Nutricion, Mexico City, Mexico
- Instituto de Investigaciones Biomédicas, Departamento de Medicina Genómica y Toxicología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Frederick E Dewey
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Aris Baras
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Christian Gieger
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Technische Universität München, Munich, Germany
- Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Deutsches Forschungszentrum für Herz-Kreislauferkrankungen (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Konstantin Strauch
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Medical Informatics, Biometry and Epidemiology, Chair of Genetic Epidemiology, Ludwig-Maximilians-Universität, Neuherberg, Germany
| | - Leslie Lange
- Department of Medicine, University of Colorado Denver, Aurora, CO, USA
| | - Niels Grarup
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
| | - Oluf Pedersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Philip Zeitler
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Dana Dabelea
- Department of Epidemiology, Colorado School of Public Health, Aurora, CO, USA
| | - Goncalo Abecasis
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Graeme I Bell
- Department of Medicine, The University of Chicago, Chicago, IL, USA
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA
| | - Nancy J Cox
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, USA
| | - Mark Seielstad
- Department of Laboratory Medicine & Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
- Blood Systems Research Institute, San Francisco, CA, USA
| | - Rob Sladek
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Division of Endocrinology and Metabolism, Department of Medicine, McGill University, Montreal, Quebec, Canada
- McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada
| | - James B Meigs
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Steve S Rich
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Jerome I Rotter
- Department of Pediatrics, Los Angeles BioMedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
- Department of Medicine, Los Angeles BioMedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
- Institute for Translational Genomics and Population Sciences, Los Angeles BioMedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - David Altshuler
- Program in Metabolism, Broad Institute, Cambridge, MA, USA
- Program in Medical & Population Genetics, Broad Institute, Cambridge, MA, USA
- Diabetes Research Center (Diabetes Unit), Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Noël P Burtt
- Program in Metabolism, Broad Institute, Cambridge, MA, USA
- Program in Medical & Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Laura J Scott
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Andrew P Morris
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Department of Biostatistics, University of Liverpool, Liverpool, UK
| | - Jose C Florez
- Program in Metabolism, Broad Institute, Cambridge, MA, USA
- Program in Medical & Population Genetics, Broad Institute, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Diabetes Research Center (Diabetes Unit), Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Mark I McCarthy
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Oxford NIHR Biomedical Research Centre, Oxford University Hospitals Trust, Oxford, UK
| | - Michael Boehnke
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
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5
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Teslovich TM, Kim DS, Yin X, Stancáková A, Jackson AU, Wielscher M, Naj A, Perry JRB, Huyghe JR, Stringham HM, Davis JP, Raulerson CK, Welch RP, Fuchsberger C, Locke AE, Sim X, Chines PS, Narisu N, Kangas AJ, Soininen P, Ala-Korpela M, Gudnason V, Musani SK, Jarvelin MR, Schellenberg GD, Speliotes EK, Kuusisto J, Collins FS, Boehnke M, Laakso M, Mohlke KL. Identification of seven novel loci associated with amino acid levels using single-variant and gene-based tests in 8545 Finnish men from the METSIM study. Hum Mol Genet 2019; 27:1664-1674. [PMID: 29481666 DOI: 10.1093/hmg/ddy067] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Accepted: 02/15/2018] [Indexed: 12/13/2022] Open
Abstract
Comprehensive metabolite profiling captures many highly heritable traits, including amino acid levels, which are potentially sensitive biomarkers for disease pathogenesis. To better understand the contribution of genetic variation to amino acid levels, we performed single variant and gene-based tests of association between nine serum amino acids (alanine, glutamine, glycine, histidine, isoleucine, leucine, phenylalanine, tyrosine, and valine) and 16.6 million genotyped and imputed variants in 8545 non-diabetic Finnish men from the METabolic Syndrome In Men (METSIM) study with replication in Northern Finland Birth Cohort (NFBC1966). We identified five novel loci associated with amino acid levels (P = < 5×10-8): LOC157273/PPP1R3B with glycine (rs9987289, P = 2.3×10-26); ZFHX3 (chr16:73326579, minor allele frequency (MAF) = 0.42%, P = 3.6×10-9), LIPC (rs10468017, P = 1.5×10-8), and WWOX (rs9937914, P = 3.8×10-8) with alanine; and TRIB1 with tyrosine (rs28601761, P = 8×10-9). Gene-based tests identified two novel genes harboring missense variants of MAF <1% that show aggregate association with amino acid levels: PYCR1 with glycine (Pgene = 1.5×10-6) and BCAT2 with valine (Pgene = 7.4×10-7); neither gene was implicated by single variant association tests. These findings are among the first applications of gene-based tests to identify new loci for amino acid levels. In addition to the seven novel gene associations, we identified five independent signals at established amino acid loci, including two rare variant signals at GLDC (rs138640017, MAF=0.95%, Pconditional = 5.8×10-40) with glycine levels and HAL (rs141635447, MAF = 0.46%, Pconditional = 9.4×10-11) with histidine levels. Examination of all single variant association results in our data revealed a strong inverse relationship between effect size and MAF (Ptrend<0.001). These novel signals provide further insight into the molecular mechanisms of amino acid metabolism and potentially, their perturbations in disease.
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Affiliation(s)
- Tanya M Teslovich
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Daniel Seung Kim
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Xianyong Yin
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Alena Stancáková
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Anne U Jackson
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Matthias Wielscher
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
| | - Adam Naj
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, University of Pennsylvania, PA 19104, USA.,Departments of Biostatistics, and Epidemiology (DBE) and Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania, PA 19104, USA
| | - John R B Perry
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Jeroen R Huyghe
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Heather M Stringham
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - James P Davis
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Chelsea K Raulerson
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Ryan P Welch
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Christian Fuchsberger
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Adam E Locke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Xueling Sim
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Peter S Chines
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Narisu Narisu
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Antti J Kangas
- Computational Medicine, Faculty of Medicine, University of Oulu and Biocenter Oulu, Oulu, Finland
| | - Pasi Soininen
- Computational Medicine, Faculty of Medicine, University of Oulu and Biocenter Oulu, Oulu, Finland.,NMR Metabolomics Laboratory, School of Pharmacy, University of Eastern Finland, Kuopio, Finland
| | | | - Mika Ala-Korpela
- Computational Medicine, Faculty of Medicine, University of Oulu and Biocenter Oulu, Oulu, Finland.,NMR Metabolomics Laboratory, School of Pharmacy, University of Eastern Finland, Kuopio, Finland.,Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK.,Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK.,Systems Epidemiology, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia.,Department of Epidemiology and Preventive Medicine, Faculty of Medicine, Nursing and Health Sciences, School of Public Health and Preventive Medicine, The Alfred Hospital, Monash University, Melbourne, VIC, Australia
| | - Vilmundur Gudnason
- Icelandic Heart Association and the Faculty of Medicine, University of Iceland, Kopavogur, Iceland
| | - Solomon K Musani
- University of Mississippi Medical Center, Jackson, MS 39213, USA
| | - Marjo-Riitta Jarvelin
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, UK.,Center for Life Course Health Research, Faculty of Medicine, University of Oulu, 90014 Oulu, Finland.,Biocenter Oulu, University of Oulu, 90014 Oulu, Finland.,Unit of Primary Care, Oulu University Hospital, Oulu, Finland
| | - Gerard D Schellenberg
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, University of Pennsylvania, PA 19104, USA
| | - Elizabeth K Speliotes
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Johanna Kuusisto
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Francis S Collins
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Markku Laakso
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
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6
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Taylor DL, Knowles DA, Scott LJ, Ramirez AH, Casale FP, Wolford BN, Guan L, Varshney A, Albanus RD, Parker SCJ, Narisu N, Chines PS, Erdos MR, Welch RP, Kinnunen L, Saramies J, Sundvall J, Lakka TA, Laakso M, Tuomilehto J, Koistinen HA, Stegle O, Boehnke M, Birney E, Collins FS. Interactions between genetic variation and cellular environment in skeletal muscle gene expression. PLoS One 2018; 13:e0195788. [PMID: 29659628 PMCID: PMC5901994 DOI: 10.1371/journal.pone.0195788] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 03/29/2018] [Indexed: 12/18/2022] Open
Abstract
From whole organisms to individual cells, responses to environmental conditions are influenced by genetic makeup, where the effect of genetic variation on a trait depends on the environmental context. RNA-sequencing quantifies gene expression as a molecular trait, and is capable of capturing both genetic and environmental effects. In this study, we explore opportunities of using allele-specific expression (ASE) to discover cis-acting genotype-environment interactions (GxE)—genetic effects on gene expression that depend on an environmental condition. Treating 17 common, clinical traits as approximations of the cellular environment of 267 skeletal muscle biopsies, we identify 10 candidate environmental response expression quantitative trait loci (reQTLs) across 6 traits (12 unique gene-environment trait pairs; 10% FDR per trait) including sex, systolic blood pressure, and low-density lipoprotein cholesterol. Although using ASE is in principle a promising approach to detect GxE effects, replication of such signals can be challenging as validation requires harmonization of environmental traits across cohorts and a sufficient sampling of heterozygotes for a transcribed SNP. Comprehensive discovery and replication will require large human transcriptome datasets, or the integration of multiple transcribed SNPs, coupled with standardized clinical phenotyping.
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Affiliation(s)
- D. Leland Taylor
- National Human Genome Research Institute, National Institutes of Health, Bethesda, United States of America
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - David A. Knowles
- Department of Computer Science, Stanford University, Stanford, California, United States of America
| | - Laura J. Scott
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Andrea H. Ramirez
- Department of Medicine, Vanderbilt University Medical Center, Tennessee, United States of America
| | - Francesco Paolo Casale
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Brooke N. Wolford
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Li Guan
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Arushi Varshney
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Ricardo D’Oliveira Albanus
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Stephen C. J. Parker
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Narisu Narisu
- National Human Genome Research Institute, National Institutes of Health, Bethesda, United States of America
| | - Peter S. Chines
- National Human Genome Research Institute, National Institutes of Health, Bethesda, United States of America
| | - Michael R. Erdos
- National Human Genome Research Institute, National Institutes of Health, Bethesda, United States of America
| | - Ryan P. Welch
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Leena Kinnunen
- Department of Public Health Solutions, National Institute for Health and Welfare, Helsinki, Finland
| | - Jouko Saramies
- South Karelia Social and Health Care District, Lappeenranta, Finland
| | - Jouko Sundvall
- Department of Public Health Solutions, National Institute for Health and Welfare, Helsinki, Finland
| | - Timo A. Lakka
- Institute of Biomedicine/Physiology, University of Eastern Finland, Kuopio, Finland
- Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
- Department of Clinical Physiology and Nuclear Medicine, Kuopio University Hospital, University of Eastern Finland, Kuopio, Finland
| | - Markku Laakso
- Department of Medicine, University of Eastern Finland, Kuopio, Finland
- Kuopio University Hospital, Kuopio, Finland
| | - Jaakko Tuomilehto
- Department of Public Health Solutions, National Institute for Health and Welfare, Helsinki, Finland
- Department of Neurosciences and Preventive Medicine, Danube University Krems, Krems, Austria
- Diabetes Research Group, King Abdulaziz University, Jeddah, Saudi Arabia
- Dasman Diabetes Institute, Dasman, Kuwait
| | - Heikki A. Koistinen
- Department of Public Health Solutions, National Institute for Health and Welfare, Helsinki, Finland
- Department of Medicine and Abdominal Center: Endocrinology, University of Helsinki and Helsinki University Central Hospital, Haartmaninkatu 4, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, Biomedicum 2U, Tukholmankatu 8, Helsinki, Finland
| | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
- * E-mail: (EB); (FSC)
| | - Francis S. Collins
- National Human Genome Research Institute, National Institutes of Health, Bethesda, United States of America
- * E-mail: (EB); (FSC)
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7
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Kycia I, Wolford BN, Huyghe JR, Fuchsberger C, Vadlamudi S, Kursawe R, Welch RP, Albanus RD, Uyar A, Khetan S, Lawlor N, Bolisetty M, Mathur A, Kuusisto J, Laakso M, Ucar D, Mohlke KL, Boehnke M, Collins FS, Parker SCJ, Stitzel ML. A Common Type 2 Diabetes Risk Variant Potentiates Activity of an Evolutionarily Conserved Islet Stretch Enhancer and Increases C2CD4A and C2CD4B Expression. Am J Hum Genet 2018; 102:620-635. [PMID: 29625024 DOI: 10.1016/j.ajhg.2018.02.020] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 02/22/2018] [Indexed: 01/17/2023] Open
Abstract
Genome-wide association studies (GWASs) and functional genomics approaches implicate enhancer disruption in islet dysfunction and type 2 diabetes (T2D) risk. We applied genetic fine-mapping and functional (epi)genomic approaches to a T2D- and proinsulin-associated 15q22.2 locus to identify a most likely causal variant, determine its direction of effect, and elucidate plausible target genes. Fine-mapping and conditional analyses of proinsulin levels of 8,635 non-diabetic individuals from the METSIM study support a single association signal represented by a cluster of 16 strongly associated (p < 10-17) variants in high linkage disequilibrium (r2 > 0.8) with the GWAS index SNP rs7172432. These variants reside in an evolutionarily and functionally conserved islet and β cell stretch or super enhancer; the most strongly associated variant (rs7163757, p = 3 × 10-19) overlaps a conserved islet open chromatin site. DNA sequence containing the rs7163757 risk allele displayed 2-fold higher enhancer activity than the non-risk allele in reporter assays (p < 0.01) and was differentially bound by β cell nuclear extract proteins. Transcription factor NFAT specifically potentiated risk-allele enhancer activity and altered patterns of nuclear protein binding to the risk allele in vitro, suggesting that it could be a factor mediating risk-allele effects. Finally, the rs7163757 proinsulin-raising and T2D risk allele (C) was associated with increased expression of C2CD4B, and possibly C2CD4A, both of which were induced by inflammatory cytokines, in human islets. Together, these data suggest that rs7163757 contributes to genetic risk of islet dysfunction and T2D by increasing NFAT-mediated islet enhancer activity and modulating C2CD4B, and possibly C2CD4A, expression in (patho)physiologic states.
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Affiliation(s)
- Ina Kycia
- Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Brooke N Wolford
- National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Jeroen R Huyghe
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Christian Fuchsberger
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Romy Kursawe
- Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Ryan P Welch
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ricardo d'Oliveira Albanus
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Asli Uyar
- Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Shubham Khetan
- Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Nathan Lawlor
- Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Mohan Bolisetty
- Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Anubhuti Mathur
- Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Johanna Kuusisto
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, 70210 Kuopio, Finland
| | - Markku Laakso
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, 70210 Kuopio, Finland
| | - Duygu Ucar
- Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Institute of Systems Genomics, University of Connecticut Health Center, Farmington, CT 06032, USA
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Francis S Collins
- National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Stephen C J Parker
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Michael L Stitzel
- Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Institute of Systems Genomics, University of Connecticut Health Center, Farmington, CT 06032, USA.
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8
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Flannick J, Fuchsberger C, Mahajan A, Teslovich TM, Agarwala V, Gaulton KJ, Caulkins L, Koesterer R, Ma C, Moutsianas L, McCarthy DJ, Rivas MA, Perry JRB, Sim X, Blackwell TW, Robertson NR, Rayner NW, Cingolani P, Locke AE, Tajes JF, Highland HM, Dupuis J, Chines PS, Lindgren CM, Hartl C, Jackson AU, Chen H, Huyghe JR, van de Bunt M, Pearson RD, Kumar A, Müller-Nurasyid M, Grarup N, Stringham HM, Gamazon ER, Lee J, Chen Y, Scott RA, Below JE, Chen P, Huang J, Go MJ, Stitzel ML, Pasko D, Parker SCJ, Varga TV, Green T, Beer NL, Day-Williams AG, Ferreira T, Fingerlin T, Horikoshi M, Hu C, Huh I, Ikram MK, Kim BJ, Kim Y, Kim YJ, Kwon MS, Lee J, Lee S, Lin KH, Maxwell TJ, Nagai Y, Wang X, Welch RP, Yoon J, Zhang W, Barzilai N, Voight BF, Han BG, Jenkinson CP, Kuulasmaa T, Kuusisto J, Manning A, Ng MCY, Palmer ND, Balkau B, Stančáková A, Abboud HE, Boeing H, Giedraitis V, Prabhakaran D, Gottesman O, Scott J, Carey J, Kwan P, Grant G, Smith JD, Neale BM, Purcell S, Butterworth AS, Howson JMM, Lee HM, Lu Y, Kwak SH, Zhao W, Danesh J, Lam VKL, Park KS, Saleheen D, So WY, Tam CHT, Afzal U, Aguilar D, Arya R, Aung T, Chan E, Navarro C, Cheng CY, Palli D, Correa A, Curran JE, Rybin D, Farook VS, Fowler SP, Freedman BI, Griswold M, Hale DE, Hicks PJ, Khor CC, Kumar S, Lehne B, Thuillier D, Lim WY, Liu J, Loh M, Musani SK, Puppala S, Scott WR, Yengo L, Tan ST, Taylor HA, Thameem F, Wilson G, Wong TY, Njølstad PR, Levy JC, Mangino M, Bonnycastle LL, Schwarzmayr T, Fadista J, Surdulescu GL, Herder C, Groves CJ, Wieland T, Bork-Jensen J, Brandslund I, Christensen C, Koistinen HA, Doney AS.F, Kinnunen L, Esko T, Farmer AJ, Hakaste L, Hodgkiss D, Kravic J, Lyssenko V, Hollensted M, Jørgensen ME, Jørgensen T, Ladenvall C, Justesen JM, Käräjämäki A, Kriebel J, Rathmann W, Lannfelt L, Lauritzen T, Narisu N, Linneberg A, Melander O, Milani L, Neville M, Orho-Melander M, Qi L, Qi Q, Roden M, Rolandsson O, Swift A, Rosengren AH, Stirrups K, Wood AR, Mihailov E, Blancher C, Carneiro MO, Maguire J, Poplin R, Shakir K, Fennell T, DePristo M, de Angelis MH, Deloukas P, Gjesing AP, Jun G, Nilsson P, Murphy J, Onofrio R, Thorand B, Hansen T, Meisinger C, Hu FB, Isomaa B, Karpe F, Liang L, Peters A, Huth C, O'Rahilly SP, Palmer CNA, Pedersen O, Rauramaa R, Tuomilehto J, Salomaa V, Watanabe RM, Syvänen AC, Bergman RN, Bharadwaj D, Bottinger EP, Cho YS, Chandak GR, Chan JCN, Chia KS, Daly MJ, Ebrahim SB, Langenberg C, Elliott P, Jablonski KA, Lehman DM, Jia W, Ma RCW, Pollin TI, Sandhu M, Tandon N, Froguel P, Barroso I, Teo YY, Zeggini E, Loos RJF, Small KS, Ried JS, DeFronzo RA, Grallert H, Glaser B, Metspalu A, Wareham NJ, Walker M, Banks E, Gieger C, Ingelsson E, Im HK, Illig T, Franks PW, Buck G, Trakalo J, Buck D, Prokopenko I, Mägi R, Lind L, Farjoun Y, Owen KR, Gloyn AL, Strauch K, Tuomi T, Kooner JS, Lee JY, Park T, Donnelly P, Morris AD, Hattersley AT, Bowden DW, Collins FS, Atzmon G, Chambers JC, Spector TD, Laakso M, Strom TM, Bell GI, Blangero J, Duggirala R, Tai ES, McVean G, Hanis CL, Wilson JG, Seielstad M, Frayling TM, Meigs JB, Cox NJ, Sladek R, Lander ES, Gabriel S, Mohlke KL, Meitinger T, Groop L, Abecasis G, Scott LJ, Morris AP, Kang HM, Altshuler D, Burtt NP, Florez JC, Boehnke M, McCarthy MI. Erratum: Sequence data and association statistics from 12,940 type 2 diabetes cases and controls. Sci Data 2018; 5:180002. [PMID: 29360107 PMCID: PMC5779067 DOI: 10.1038/sdata.2018.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
This corrects the article DOI: 10.1038/sdata.2017.179.
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9
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Jason F, Fuchsberger C, Mahajan A, Teslovich TM, Agarwala V, Gaulton KJ, Caulkins L, Koesterer R, Ma C, Moutsianas L, McCarthy DJ, Rivas MA, Perry JRB, Sim X, Blackwell TW, Robertson NR, Rayner NW, Cingolani P, Locke AE, Tajes JF, Highland HM, Dupuis J, Chines PS, Lindgren CM, Hartl C, Jackson AU, Chen H, Huyghe JR, van de Bunt M, Pearson RD, Kumar A, Müller-Nurasyid M, Grarup N, Stringham HM, Gamazon ER, Lee J, Chen Y, Scott RA, Below JE, Chen P, Huang J, Go MJ, Stitzel ML, Pasko D, Parker SCJ, Varga TV, Green T, Beer NL, Day-Williams AG, Ferreira T, Fingerlin T, Horikoshi M, Hu C, Huh I, Ikram MK, Kim BJ, Kim Y, Kim YJ, Kwon MS, Lee J, Lee S, Lin KH, Maxwell TJ, Nagai Y, Wang X, Welch RP, Yoon J, Zhang W, Barzilai N, Voight BF, Han BG, Jenkinson CP, Kuulasmaa T, Kuusisto J, Manning A, Ng MCY, Palmer ND, Balkau B, Stančáková A, Abboud HE, Boeing H, Giedraitis V, Prabhakaran D, Gottesman O, Scott J, Carey J, Kwan P, Grant G, Smith JD, Neale BM, Purcell S, Butterworth AS, Howson JMM, Lee HM, Lu Y, Kwak SH, Zhao W, Danesh J, Lam VKL, Park KS, Saleheen D, So WY, Tam CHT, Afzal U, Aguilar D, Arya R, Aung T, Chan E, Navarro C, Cheng CY, Palli D, Correa A, Curran JE, Rybin D, Farook VS, Fowler SP, Freedman BI, Griswold M, Hale DE, Hicks PJ, Khor CC, Kumar S, Lehne B, Thuillier D, Lim WY, Liu J, Loh M, Musani SK, Puppala S, Scott WR, Yengo L, Tan ST, Taylor HA, Thameem F, Wilson G, Wong TY, Njølstad PR, Levy JC, Mangino M, Bonnycastle LL, Schwarzmayr T, Fadista J, Surdulescu GL, Herder C, Groves CJ, Wieland T, Bork-Jensen J, Brandslund I, Christensen C, Koistinen HA, Doney ASF, Kinnunen L, Esko T, Farmer AJ, Hakaste L, Hodgkiss D, Kravic J, Lyssenko V, Hollensted M, Jørgensen ME, Jørgensen T, Ladenvall C, Justesen JM, Käräjämäki A, Kriebel J, Rathmann W, Lannfelt L, Lauritzen T, Narisu N, Linneberg A, Melander O, Milani L, Neville M, Orho-Melander M, Qi L, Qi Q, Roden M, Rolandsson O, Swift A, Rosengren AH, Stirrups K, Wood AR, Mihailov E, Blancher C, Carneiro MO, Maguire J, Poplin R, Shakir K, Fennell T, DePristo M, de Angelis MH, Deloukas P, Gjesing AP, Jun G, Nilsson P, Murphy J, Onofrio R, Thorand B, Hansen T, Meisinger C, Hu FB, Isomaa B, Karpe F, Liang L, Peters A, Huth C, O'Rahilly SP, Palmer CNA, Pedersen O, Rauramaa R, Tuomilehto J, Salomaa V, Watanabe RM, Syvänen AC, Bergman RN, Bharadwaj D, Bottinger EP, Cho YS, Chandak GR, Chan JCN, Chia KS, Daly MJ, Ebrahim SB, Langenberg C, Elliott P, Jablonski KA, Lehman DM, Jia W, Ma RCW, Pollin TI, Sandhu M, Tandon N, Froguel P, Barroso I, Teo YY, Zeggini E, Loos RJF, Small KS, Ried JS, DeFronzo RA, Grallert H, Glaser B, Metspalu A, Wareham NJ, Walker M, Banks E, Gieger C, Ingelsson E, Im HK, Illig T, Franks PW, Buck G, Trakalo J, Buck D, Prokopenko I, Mägi R, Lind L, Farjoun Y, Owen KR, Gloyn AL, Strauch K, Tuomi T, Kooner JS, Lee JY, Park T, Donnelly P, Morris AD, Hattersley AT, Bowden DW, Collins FS, Atzmon G, Chambers JC, Spector TD, Laakso M, Strom TM, Bell GI, Blangero J, Duggirala R, Tai ES, McVean G, Hanis CL, Wilson JG, Seielstad M, Frayling TM, Meigs JB, Cox NJ, Sladek R, Lander ES, Gabriel S, Mohlke KL, Meitinger T, Groop L, Abecasis G, Scott LJ, Morris AP, Kang HM, Altshuler D, Burtt NP, Florez JC, Boehnke M, McCarthy MI. Sequence data and association statistics from 12,940 type 2 diabetes cases and controls. Sci Data 2017; 4:170179. [PMID: 29257133 PMCID: PMC5735917 DOI: 10.1038/sdata.2017.179] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 11/02/2017] [Indexed: 02/08/2023] Open
Abstract
To investigate the genetic basis of type 2 diabetes (T2D) to high resolution, the GoT2D and T2D-GENES consortia catalogued variation from whole-genome sequencing of 2,657 European individuals and exome sequencing of 12,940 individuals of multiple ancestries. Over 27M SNPs, indels, and structural variants were identified, including 99% of low-frequency (minor allele frequency [MAF] 0.1-5%) non-coding variants in the whole-genome sequenced individuals and 99.7% of low-frequency coding variants in the whole-exome sequenced individuals. Each variant was tested for association with T2D in the sequenced individuals, and, to increase power, most were tested in larger numbers of individuals (>80% of low-frequency coding variants in ~82 K Europeans via the exome chip, and ~90% of low-frequency non-coding variants in ~44 K Europeans via genotype imputation). The variants, genotypes, and association statistics from these analyses provide the largest reference to date of human genetic information relevant to T2D, for use in activities such as T2D-focused genotype imputation, functional characterization of variants or genes, and other novel analyses to detect associations between sequence variation and T2D.
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Affiliation(s)
- Flannick Jason
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA,Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA,
J.F. ()
| | - Christian Fuchsberger
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | - Anubha Mahajan
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Tanya M. Teslovich
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | - Vineeta Agarwala
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA,Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Kyle J. Gaulton
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Lizz Caulkins
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA
| | - Ryan Koesterer
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA
| | - Clement Ma
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | - Loukas Moutsianas
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Davis J. McCarthy
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK,Department of Statistics, University of Oxford, Oxford, UK
| | - Manuel A. Rivas
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - John R. B. Perry
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK,Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, UK,MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK,Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Xueling Sim
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | - Thomas W. Blackwell
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | - Neil R. Robertson
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK,Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - N William Rayner
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK,Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK,Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Pablo Cingolani
- School of Computer Science, McGill University, Montreal, Quebec, Canada,McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada
| | - Adam E. Locke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | - Juan Fernandez Tajes
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Heather M. Highland
- Human Genetics Center, The University of Texas Graduate School of Biomedical Sciences at Houston, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Josee Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, USA,National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, Massachusetts, USA
| | - Peter S. Chines
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Cecilia M. Lindgren
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA,Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Christopher Hartl
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA
| | - Anne U. Jackson
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | - Han Chen
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, USA,Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Jeroen R. Huyghe
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | - Martijn van de Bunt
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK,Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Richard D. Pearson
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Ashish Kumar
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK,Chronic Disease Epidemiology, Swiss Tropical and Public Health Institute, University of Basel, Basel, Switzerland
| | - Martina Müller-Nurasyid
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany,Department of Medicine I, University Hospital Grosshadern, Ludwig-Maximilians-Universität, Munich, Germany,Chair of Genetic Epidemiology, IBE, Faculty of Medicine, LMU Munich, Germany,DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany
| | - Niels Grarup
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Heather M. Stringham
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | - Eric R. Gamazon
- Department of Medicine, Section of Genetic Medicine, The University of Chicago, Chicago, Illinois, USA
| | - Jaehoon Lee
- Department of Statistics, Seoul National University, Seoul, Republic of Korea
| | - Yuhui Chen
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Robert A. Scott
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Jennifer E. Below
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Peng Chen
- Saw Swee Hock School of Public Health, National University of Singapore, National University Health System, Singapore, Singapore
| | - Jinyan Huang
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Min Jin Go
- Center for Genome Science, Korea National Institute of Health, Chungcheongbuk-do, Republic of Korea
| | - Michael L. Stitzel
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
| | - Dorota Pasko
- Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Stephen C. J. Parker
- Departments of Computational Medicine & Bioinformatics and Human Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | - Tibor V. Varga
- Department of Clinical Sciences, Lund University Diabetes Centre, Genetic and Molecular Epidemiology Unit, Lund University, Malmö, Sweden
| | - Todd Green
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA
| | - Nicola L. Beer
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Aaron G. Day-Williams
- Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Teresa Ferreira
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Tasha Fingerlin
- Department of Epidemiology, Colorado School of Public Health, University of Colorado, Aurora, Colorado, USA
| | - Momoko Horikoshi
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK,Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Cheng Hu
- Department of Endocrinology and Metabolism, Shanghai Diabetes Institute, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Iksoo Huh
- Department of Statistics, Seoul National University, Seoul, Republic of Korea
| | - Mohammad Kamran Ikram
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore,Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, Singapore, Singapore,The Eye Academic Clinical Programme, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Bong-Jo Kim
- Center for Genome Science, Korea National Institute of Health, Chungcheongbuk-do, Republic of Korea
| | - Yongkang Kim
- Department of Statistics, Seoul National University, Seoul, Republic of Korea
| | - Young Jin Kim
- Center for Genome Science, Korea National Institute of Health, Chungcheongbuk-do, Republic of Korea
| | - Min-Seok Kwon
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | - Juyoung Lee
- Center for Genome Science, Korea National Institute of Health, Chungcheongbuk-do, Republic of Korea
| | - Selyeong Lee
- Department of Statistics, Seoul National University, Seoul, Republic of Korea
| | - Keng-Han Lin
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | - Taylor J. Maxwell
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Yoshihiko Nagai
- McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada,Department of Human Genetics, McGill University, Montreal, Quebec, Canada,Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Xu Wang
- Saw Swee Hock School of Public Health, National University of Singapore, National University Health System, Singapore, Singapore
| | - Ryan P. Welch
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | - Joon Yoon
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | - Weihua Zhang
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK,Department of Cardiology, Ealing Hospital NHS Trust, Southall, Middlesex, UK
| | - Nir Barzilai
- Departments of Medicine and Genetics, Albert Einstein College of Medicine, New York, USA
| | - Benjamin F. Voight
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania—Perelman School of Medicine, Philadelphia, Pennsylvania, USA,Department of Genetics, University of Pennsylvania—Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Bok-Ghee Han
- Center for Genome Science, Korea National Institute of Health, Chungcheongbuk-do, Republic of Korea
| | - Christopher P. Jenkinson
- Department of Medicine, University of Texas Health Science Center, San Antonio, Texas, USA,Research, South Texas Veterans Health Care System, San Antonio, Texas, USA
| | - Teemu Kuulasmaa
- Faculty of Health Sciences, Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland
| | - Johanna Kuusisto
- Faculty of Health Sciences, Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland,Kuopio University Hospital, Kuopio, Finland
| | - Alisa Manning
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA
| | - Maggie C. Y. Ng
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA,Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Nicholette D. Palmer
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA,Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA,Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Beverley Balkau
- Centre for Research in Epidemiology and Population Health, Inserm U1018, Villejuif, France
| | - Alena Stančáková
- Faculty of Health Sciences, Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland
| | - Hanna E. Abboud
- Department of Medicine, University of Texas Health Science Center, San Antonio, Texas, USA
| | - Heiner Boeing
- German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
| | - Vilmantas Giedraitis
- Department of Public Health and Caring Sciences, Geriatrics, Uppsala University, Uppsala, Sweden
| | | | - Omri Gottesman
- The Charles Bronfman Institute for Personalized Medicine, The Icahn School of Medicine at Mount Sinai, New York, USA
| | - James Scott
- National Heart and Lung Institute, Cardiovascular Sciences, Hammersmith Campus, Imperial College London, London, UK
| | - Jason Carey
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA
| | - Phoenix Kwan
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | - George Grant
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA
| | - Joshua D. Smith
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
| | - Benjamin M. Neale
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA,Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Shaun Purcell
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA,Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA,Department of Psychiatry, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Adam S. Butterworth
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Joanna M. M. Howson
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Heung Man Lee
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Yingchang Lu
- The Charles Bronfman Institute for Personalized Medicine, The Icahn School of Medicine at Mount Sinai, New York, USA
| | - Soo-Heon Kwak
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Wei Zhao
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - John Danesh
- Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK,Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK,NIHR Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Vincent K. L. Lam
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Kyong Soo Park
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, and College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Danish Saleheen
- Department of Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA,Center for Non-Communicable Diseases, Karachi, Pakistan
| | - Wing Yee So
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Claudia H. T. Tam
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Uzma Afzal
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
| | - David Aguilar
- Cardiovascular Division, Baylor College of Medicine, Houston, Texas, USA
| | - Rector Arya
- Department of Pediatrics, University of Texas Health Science Center, San Antonio, Texas, USA
| | - Tin Aung
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore,Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, Singapore, Singapore,The Eye Academic Clinical Programme, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Edmund Chan
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, Singapore, Singapore
| | - Carmen Navarro
- Department of Epidemiology, Murcia Regional Health Council, IMIB-Arrixaca, Murcia, Spain,CIBER Epidemiología y Salud Pública (CIBERESP), Spain,Unit of Preventive Medicine and Public Health, School of Medicine, University of Murcia, Spain
| | - Ching-Yu Cheng
- Saw Swee Hock School of Public Health, National University of Singapore, National University Health System, Singapore, Singapore,Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore,Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, Singapore, Singapore,The Eye Academic Clinical Programme, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Domenico Palli
- Cancer Research and Prevention Institute (ISPO), Florence, Italy
| | - Adolfo Correa
- Department of Medicine, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Joanne E. Curran
- South Texas Diabetes and Obesity Institute, Regional Academic Health Center, University of Texas Health Science Center at San Antonio/University of Texas Rio Grande Valley, Brownsville, Texas, USA
| | - Dennis Rybin
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, USA
| | - Vidya S. Farook
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Sharon P. Fowler
- Department of Medicine, University of Texas Health Science Center, San Antonio, Texas, USA
| | - Barry I. Freedman
- Department of Internal Medicine, Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Michael Griswold
- Center of Biostatistics and Bioinformatics, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Daniel Esten Hale
- Department of Pediatrics, University of Texas Health Science Center, San Antonio, Texas, USA
| | - Pamela J. Hicks
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA,Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA,Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Chiea-Chuen Khor
- Saw Swee Hock School of Public Health, National University of Singapore, National University Health System, Singapore, Singapore,Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore,Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, Singapore, Singapore,Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, Singapore, Singapore,Division of Human Genetics, Genome Institute of Singapore, A*STAR, Singapore, Singapore
| | - Satish Kumar
- South Texas Diabetes and Obesity Institute, Regional Academic Health Center, University of Texas Health Science Center at San Antonio/University of Texas Rio Grande Valley, Brownsville, Texas, USA
| | - Benjamin Lehne
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
| | | | - Wei Yen Lim
- Saw Swee Hock School of Public Health, National University of Singapore, National University Health System, Singapore, Singapore
| | - Jianjun Liu
- Saw Swee Hock School of Public Health, National University of Singapore, National University Health System, Singapore, Singapore,Division of Human Genetics, Genome Institute of Singapore, A*STAR, Singapore, Singapore
| | - Marie Loh
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK,Institute of Health Sciences, University of Oulu, Oulu, Finland,Translational Laboratory in Genetic Medicine (TLGM), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Solomon K. Musani
- Jackson Heart Study, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Sobha Puppala
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - William R. Scott
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
| | - Loïc Yengo
- CNRS-UMR8199, Lille University, Lille Pasteur Institute, Lille, France
| | - Sian-Tsung Tan
- Department of Cardiology, Ealing Hospital NHS Trust, Southall, Middlesex, UK,National Heart and Lung Institute, Cardiovascular Sciences, Hammersmith Campus, Imperial College London, London, UK
| | - Herman A. Taylor
- Department of Medicine, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Farook Thameem
- Department of Medicine, University of Texas Health Science Center, San Antonio, Texas, USA
| | - Gregory Wilson
- College of Public Services, Jackson State University, Jackson, Mississippi, USA
| | - Tien Yin Wong
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore,Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, Singapore, Singapore,The Eye Academic Clinical Programme, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Pål Rasmus Njølstad
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway,Department of Pediatrics, Haukeland University Hospital, Bergen, Norway
| | - Jonathan C. Levy
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Massimo Mangino
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK,NIHR Biomedical Research Centre at Guy’s and St Thomas’ Foundation Trust, London, UK
| | - Lori L. Bonnycastle
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Thomas Schwarzmayr
- Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - João Fadista
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University Diabetes Centre, Malmö, Sweden
| | | | - Christian Herder
- Institute of Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University, Düsseldorf, Germany,German Center for Diabetes Research (DZD), München-Neuherberg, Germany
| | - Christopher J. Groves
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Thomas Wieland
- Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Jette Bork-Jensen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ivan Brandslund
- Institute 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
| | - Heikki A. Koistinen
- Department of Health, National Institute for Health and Welfare, Helsinki, Finland,Abdominal Center: Endocrinology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland,Minerva Foundation Institute for Medical Research, Helsinki, Finland,Department of Medicine, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Alex S. F. Doney
- Division of Cardiovascular and Diabetes Medicine, Medical Research Institute, Ninewells Hospital and Medical School, Dundee, UK
| | - Leena Kinnunen
- Department of Health, National Institute for Health and Welfare, Helsinki, Finland
| | - Tõnu Esko
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA,Estonian Genome Center, University of Tartu, Tartu, Estonia,Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA,Division of Endocrinology, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Andrew J. Farmer
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK
| | - Liisa Hakaste
- Abdominal Center: Endocrinology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland,Folkhälsan Research Centre, Helsinki, Finland,Research Programs Unit, Diabetes and Obesity, University of Helsinki, Helsinki, Finland
| | - Dylan Hodgkiss
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Jasmina Kravic
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University Diabetes Centre, Malmö, Sweden
| | - Valeri Lyssenko
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University Diabetes Centre, Malmö, Sweden
| | - Mette Hollensted
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Torben Jørgensen
- Research Centre for Prevention and Health, Capital Region of Denmark, Glostrup, Denmark,Department of Public Health, Institute of Health Sciences, University of Copenhagen, Copenhagen, Denmark,Faculty of Medicine, Aalborg University, Aalborg, Denmark
| | - Claes Ladenvall
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University Diabetes Centre, Malmö, Sweden
| | - Johanne Marie Justesen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Annemari Käräjämäki
- Department of Primary Health Care, Vaasa Central Hospital, Vaasa, Finland,Diabetes Center, Vaasa Health Care Center, Vaasa, Finland
| | - Jennifer Kriebel
- German Center for Diabetes Research (DZD), München-Neuherberg, Germany,Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany,Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Wolfgang Rathmann
- German Center for Diabetes Research (DZD), München-Neuherberg, Germany,Institute for Biometrics and Epidemiology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University, Düsseldorf, Germany
| | - Lars Lannfelt
- Department of Public Health and Caring Sciences, Geriatrics, Uppsala University, Uppsala, Sweden
| | - Torsten Lauritzen
- Department of Public Health, Section of General Practice, Aarhus University, Aarhus, Denmark
| | - Narisu Narisu
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Allan Linneberg
- Research Centre for Prevention and Health, Capital Region of Denmark, 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
| | - Olle Melander
- Department of Clinical Sciences, Hypertension and Cardiovascular Disease, Lund University, Malmö, Sweden
| | - Lili Milani
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Matt Neville
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK,Oxford NIHR Biomedical Research Centre, Oxford University Hospitals Trust, Oxford, UK
| | - Marju Orho-Melander
- Department of Clinical Sciences, Diabetes and Cardiovascular Disease, Genetic Epidemiology, Lund University, Malmö, Sweden
| | - Lu Qi
- Department of Nutrition, Harvard School of Public Health, Boston, Massachusetts, USA,Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Qibin Qi
- Department of Nutrition, Harvard School of Public Health, Boston, Massachusetts, USA,Department of Epidemiology and Population Health, Albert Einstein College of Medicine, New York, USA
| | - 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 (DZD), München-Neuherberg, Germany,Division of Endocrinology and Diabetology, Medical Faculty, Heinrich-Heine University, Düsseldorf, Germany
| | - Olov Rolandsson
- Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
| | - Amy Swift
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Anders H. Rosengren
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University Diabetes Centre, Malmö, Sweden
| | - Kathleen Stirrups
- Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Andrew R. Wood
- Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, UK
| | | | - Christine Blancher
- High Throughput Genomics, Oxford Genomics Centre, Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Mauricio O. Carneiro
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA
| | - Jared Maguire
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA
| | - Ryan Poplin
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA
| | - Khalid Shakir
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA
| | - Timothy Fennell
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA
| | - Mark DePristo
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA
| | - Martin Hrabé de Angelis
- German Center for Diabetes Research (DZD), München-Neuherberg, Germany,Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany,Center of Life and Food Sciences Weihenstephan, Technische Universität München, Freising-Weihenstephan, Germany
| | - Panos Deloukas
- Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK,William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK,Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD), King Abdulaziz University, Jeddah, Saudi Arabia
| | - Anette P. Gjesing
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Goo Jun
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA,Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Peter Nilsson
- Department of Clinical Sciences, Medicine, Lund University, Malmö, Sweden
| | - Jacquelyn Murphy
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA
| | - Robert Onofrio
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA
| | - Barbara Thorand
- German Center for Diabetes Research (DZD), München-Neuherberg, Germany,Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - 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
| | - Christa Meisinger
- German Center for Diabetes Research (DZD), München-Neuherberg, Germany,Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Frank B. Hu
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA,Department of Nutrition, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Bo Isomaa
- Folkhälsan Research Centre, Helsinki, Finland,Department of Social Services and Health Care, Jakobstad, Finland
| | - Fredrik Karpe
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK,Oxford NIHR Biomedical Research Centre, Oxford University Hospitals Trust, Oxford, UK
| | - Liming Liang
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, USA,Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Annette Peters
- DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany,German Center for Diabetes Research (DZD), München-Neuherberg, Germany,Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Cornelia Huth
- German Center for Diabetes Research (DZD), München-Neuherberg, Germany,Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Stephen P O'Rahilly
- Metabolic Research Laboratories, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Colin N. A. Palmer
- Pat Macpherson Centre for Pharmacogenetics and Pharmacogenomics, Medical Research Institute, Ninewells Hospital and Medical School, Dundee, UK
| | - Oluf Pedersen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rainer Rauramaa
- Foundation for Research in Health, Exercise and Nutrition, Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
| | - Jaakko Tuomilehto
- Center for Vascular Prevention, Danube University Krems, Krems, Austria,Diabetes Research Group, King Abdulaziz University, Jeddah, Saudi Arabia,Dasman Diabetes Institute, Dasman, Kuwait,National Institute for Health and Welfare, Helsinki, Finland
| | - Veikko Salomaa
- National Institute for Health and Welfare, Helsinki, Finland
| | - Richard M. Watanabe
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA,Department of Physiology & Biophysics, Keck School of Medicine, University of Southern California, Los Angeles, California, USA,Diabetes and Obesity Research Institute, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Ann-Christine Syvänen
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Richard N. Bergman
- Cedars-Sinai Diabetes and Obesity Research Institute, Los Angeles, California, USA
| | - Dwaipayan Bharadwaj
- Functional Genomics Unit, CSIR-Institute of Genomics & Integrative Biology (CSIR-IGIB), New Delhi, India
| | - Erwin P. Bottinger
- The Charles Bronfman Institute for Personalized Medicine, The Icahn School of Medicine at Mount Sinai, New York, USA
| | - Yoon Shin Cho
- Department of Biomedical Science, Hallym University, Chuncheon, Republic of Korea
| | - Giriraj R. Chandak
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, India
| | - Juliana CN 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
| | - Kee Seng Chia
- Saw Swee Hock School of Public Health, National University of Singapore, National University Health System, Singapore, Singapore
| | - Mark J. Daly
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | | | - Claudia Langenberg
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Paul Elliott
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK,MRC-PHE Centre for Environment and Health, Imperial College London, London, UK
| | - Kathleen A. Jablonski
- The Biostatistics Center, The George Washington University, Rockville, Maryland, USA
| | - Donna M. Lehman
- Department of Medicine, University of Texas Health Science Center, San Antonio, Texas, USA
| | - 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
| | - Toni I. Pollin
- Department of Medicine, Division of Endocrinology, Diabetes and Nutrition, and Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Manjinder Sandhu
- Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK,Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Nikhil Tandon
- Department of Endocrinology and Metabolism, All India Institute of Medical Sciences, New Delhi, India
| | - Philippe Froguel
- CNRS-UMR8199, Lille University, Lille Pasteur Institute, Lille, France,Department of Genomics of Common Disease, School of Public Health, Imperial College London, London, UK
| | - Inês Barroso
- Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK,Metabolic Research Laboratories, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Yik Ying Teo
- Saw Swee Hock School of Public Health, National University of Singapore, National University Health System, Singapore, Singapore,Life Sciences Institute, National University of Singapore, Singapore, Singapore,Department of Statistics and Applied Probability, National University of Singapore, Singapore, Singapore
| | - Eleftheria Zeggini
- Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Ruth J. F. Loos
- The Charles Bronfman Institute for Personalized Medicine, The Icahn School of Medicine at Mount Sinai, New York, USA
| | - Kerrin S. Small
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Janina S. Ried
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Ralph A. DeFronzo
- Department of Medicine, University of Texas Health Science Center, San Antonio, Texas, USA
| | - Harald Grallert
- German Center for Diabetes Research (DZD), München-Neuherberg, Germany,Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany,Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Benjamin Glaser
- Endocrinology and Metabolism Service, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | | | - Nicholas J. Wareham
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Mark Walker
- The Medical School, Institute of Cellular Medicine, Newcastle University, Newcastle, UK
| | - Eric Banks
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA
| | - Christian Gieger
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany,Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany,Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Erik Ingelsson
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK,Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Hae Kyung Im
- Department of Medicine, Section of Genetic Medicine, The University of Chicago, Chicago, Illinois, USA
| | - Thomas Illig
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany,Hannover Unified Biobank, Hannover Medical School, Hanover, Germany,Department of Human Genetics, Hannover Medical School, Hanover, Germany
| | - Paul W. Franks
- Department of Clinical Sciences, Lund University Diabetes Centre, Genetic and Molecular Epidemiology Unit, Lund University, Malmö, Sweden,Department of Nutrition, Harvard School of Public Health, Boston, Massachusetts, USA,Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
| | - Gemma Buck
- High Throughput Genomics, Oxford Genomics Centre, Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Joseph Trakalo
- High Throughput Genomics, Oxford Genomics Centre, Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - David Buck
- High Throughput Genomics, Oxford Genomics Centre, Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Inga Prokopenko
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK,Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK,Department of Genomics of Common Disease, School of Public Health, Imperial College London, London, UK
| | - Reedik Mägi
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Lars Lind
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Yossi Farjoun
- Data Sciences and Data Engineering, Broad Institute, Cambridge, Massachusetts, USA
| | - Katharine R. Owen
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK,Oxford NIHR Biomedical Research Centre, Oxford University Hospitals Trust, Oxford, UK
| | - Anna L. Gloyn
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK,Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK,Oxford NIHR Biomedical Research Centre, Oxford University Hospitals Trust, Oxford, UK
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany,Chair of Genetic Epidemiology, IBE, Faculty of Medicine, LMU Munich, Germany
| | - Tiinamaija Tuomi
- Abdominal Center: Endocrinology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland,Folkhälsan Research Centre, Helsinki, Finland,Research Programs Unit, Diabetes and Obesity, University of Helsinki, Helsinki, Finland,Finnish Institute for Molecular Medicine, University of Helsinki, Helsinki, Finland
| | - Jaspal Singh Kooner
- Department of Cardiology, Ealing Hospital NHS Trust, Southall, Middlesex, UK,National Heart and Lung Institute, Cardiovascular Sciences, Hammersmith Campus, Imperial College London, London, UK,Imperial College Healthcare NHS Trust, Imperial College London, London, UK
| | - Jong-Young Lee
- Center for Genome Science, Korea National Institute of Health, Chungcheongbuk-do, Republic of Korea
| | - Taesung Park
- Department of Statistics, Seoul National University, Seoul, Republic of Korea,Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | - Peter Donnelly
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK,Department of Statistics, University of Oxford, Oxford, UK
| | - Andrew D. Morris
- Clinical Research Centre, Centre for Molecular Medicine, Ninewells Hospital and Medical School, Dundee, UK,The Usher Institute to the Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | | | - Donald W. Bowden
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA,Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA,Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Francis S. Collins
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Gil Atzmon
- Departments of Medicine and Genetics, Albert Einstein College of Medicine, New York, USA,Department of Natural Science, University of Haifa, Haifa, Israel
| | - John C. Chambers
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK,Department of Cardiology, Ealing Hospital NHS Trust, Southall, Middlesex, UK,Imperial College Healthcare NHS Trust, Imperial College London, London, UK
| | - Timothy D. Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Markku Laakso
- Faculty of Health Sciences, Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland,Kuopio University Hospital, Kuopio, Finland
| | - 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, Munich, Germany
| | - Graeme I. Bell
- Departments of Medicine and Human Genetics, The University of Chicago, Chicago, Illinois, USA
| | - John Blangero
- South Texas Diabetes and Obesity Institute, Regional Academic Health Center, University of Texas Health Science Center at San Antonio/University of Texas Rio Grande Valley, Brownsville, Texas, USA
| | | | - E. Shyong Tai
- Saw Swee Hock School of Public Health, National University of Singapore, National University Health System, Singapore, Singapore,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, Singapore, Singapore,Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School Singapore, Singapore, Singapore
| | - Gilean McVean
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK,Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Craig L. Hanis
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - James G. Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Mark Seielstad
- Department of Laboratory Medicine & Institute for Human Genetics, University of California, San Francisco, San Francisco, California, USA,Blood Systems Research Institute, San Francisco, California, USA
| | - Timothy M. Frayling
- Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - James B. Meigs
- General Medicine Division, Massachusetts General Hospital and Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Nancy J. Cox
- Department of Medicine, Section of Genetic Medicine, The University of Chicago, Chicago, Illinois, USA
| | - Rob Sladek
- McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada,Department of Human Genetics, McGill University, Montreal, Quebec, Canada,Division of Endocrinology and Metabolism, Department of Medicine, McGill University, Montreal, Quebec, Canada
| | - Eric S. Lander
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Stacey Gabriel
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA
| | - Karen L. Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Thomas Meitinger
- Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany,Institute of Human Genetics, Technische Universität München, Munich, Germany
| | - Leif Groop
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University Diabetes Centre, Malmö, Sweden,Finnish Institute for Molecular Medicine, University of Helsinki, Helsinki, Finland
| | - Goncalo Abecasis
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | - Laura J. Scott
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | - Andrew P. Morris
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK,Estonian Genome Center, University of Tartu, Tartu, Estonia,Department of Biostatistics, University of Liverpool, Liverpool, UK
| | - Hyun Min Kang
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - David Altshuler
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA,Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA,Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA,Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA,Diabetes Research Center (Diabetes Unit), Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Noël P. Burtt
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA
| | - Jose C. Florez
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA,Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA,Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA,Diabetes Research Center (Diabetes Unit), Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | - Mark I. McCarthy
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK,Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK,Oxford NIHR Biomedical Research Centre, Oxford University Hospitals Trust, Oxford, UK
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10
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Roman TS, Cannon ME, Vadlamudi S, Buchkovich ML, Wolford BN, Welch RP, Morken MA, Kwon GJ, Varshney A, Kursawe R, Wu Y, Jackson AU, Erdos MR, Kuusisto J, Laakso M, Scott LJ, Boehnke M, Collins FS, Parker SCJ, Stitzel ML, Mohlke KL. A Type 2 Diabetes-Associated Functional Regulatory Variant in a Pancreatic Islet Enhancer at the ADCY5 Locus. Diabetes 2017; 66:2521-2530. [PMID: 28684635 PMCID: PMC5860374 DOI: 10.2337/db17-0464] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 06/22/2017] [Indexed: 12/13/2022]
Abstract
Molecular mechanisms remain unknown for most type 2 diabetes genome-wide association study identified loci. Variants associated with type 2 diabetes and fasting glucose levels reside in introns of ADCY5, a gene that encodes adenylate cyclase 5. Adenylate cyclase 5 catalyzes the production of cyclic AMP, which is a second messenger molecule involved in cell signaling and pancreatic β-cell insulin secretion. We demonstrated that type 2 diabetes risk alleles are associated with decreased ADCY5 expression in human islets and examined candidate variants for regulatory function. rs11708067 overlaps a predicted enhancer region in pancreatic islets. The type 2 diabetes risk rs11708067-A allele showed fewer H3K27ac ChIP-seq reads in human islets, lower transcriptional activity in reporter assays in rodent β-cells (rat 832/13 and mouse MIN6), and increased nuclear protein binding compared with the rs11708067-G allele. Homozygous deletion of the orthologous enhancer region in 832/13 cells resulted in a 64% reduction in expression level of Adcy5, but not adjacent gene Sec22a, and a 39% reduction in insulin secretion. Together, these data suggest that rs11708067-A risk allele contributes to type 2 diabetes by disrupting an islet enhancer, which results in reduced ADCY5 expression and impaired insulin secretion.
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Affiliation(s)
- Tamara S Roman
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Maren E Cannon
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | - Martin L Buchkovich
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Brooke N Wolford
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Ryan P Welch
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Mario A Morken
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Grace J Kwon
- The Jackson Laboratory for Genomic Medicine, Farmington, CT
- Department of Genetics and Genome Sciences, University of Connecticut Health, Farmington, CT
| | - Arushi Varshney
- Department of Human Genetics, University of Michigan, Ann Arbor, MI
| | - Romy Kursawe
- The Jackson Laboratory for Genomic Medicine, Farmington, CT
| | - Ying Wu
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Anne U Jackson
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, MI
| | | | - Michael R Erdos
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Johanna Kuusisto
- Internal Medicine, Institute of Clinical Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Markku Laakso
- Internal Medicine, Institute of Clinical Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Laura J Scott
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Francis S Collins
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Stephen C J Parker
- Department of Human Genetics, University of Michigan, Ann Arbor, MI
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI
| | - Michael L Stitzel
- The Jackson Laboratory for Genomic Medicine, Farmington, CT
- Institute for Systems Genomics, University of Connecticut, Farmington, CT
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
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11
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Cavalcante RG, Lee C, Welch RP, Patil S, Weymouth T, Scott LJ, Sartor MA. Broad-Enrich: functional interpretation of large sets of broad genomic regions. ACTA ACUST UNITED AC 2015; 30:i393-400. [PMID: 25161225 PMCID: PMC4147897 DOI: 10.1093/bioinformatics/btu444] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Motivation: Functional enrichment testing facilitates the interpretation of Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) data in terms of pathways and other biological contexts. Previous methods developed and used to test for key gene sets affected in ChIP-seq experiments treat peaks as points, and are based on the number of peaks associated with a gene or a binary score for each gene. These approaches work well for transcription factors, but histone modifications often occur over broad domains, and across multiple genes. Results: To incorporate the unique properties of broad domains into functional enrichment testing, we developed Broad-Enrich, a method that uses the proportion of each gene’s locus covered by a peak. We show that our method has a well-calibrated false-positive rate, performing well with ChIP-seq data having broad domains compared with alternative approaches. We illustrate Broad-Enrich with 55 ENCODE ChIP-seq datasets using different methods to define gene loci. Broad-Enrich can also be applied to other datasets consisting of broad genomic domains such as copy number variations. Availability and implementation:http://broad-enrich.med.umich.edu for Web version and R package. Contact:sartorma@umich.edu Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Raymond G Cavalcante
- Department of Computational Medicine and Bioinformatics, Department of Biostatistics and Center of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Chee Lee
- Department of Computational Medicine and Bioinformatics, Department of Biostatistics and Center of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ryan P Welch
- Department of Computational Medicine and Bioinformatics, Department of Biostatistics and Center of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA Department of Computational Medicine and Bioinformatics, Department of Biostatistics and Center of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Snehal Patil
- Department of Computational Medicine and Bioinformatics, Department of Biostatistics and Center of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Terry Weymouth
- Department of Computational Medicine and Bioinformatics, Department of Biostatistics and Center of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Laura J Scott
- Department of Computational Medicine and Bioinformatics, Department of Biostatistics and Center of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Maureen A Sartor
- Department of Computational Medicine and Bioinformatics, Department of Biostatistics and Center of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA Department of Computational Medicine and Bioinformatics, Department of Biostatistics and Center of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA Department of Computational Medicine and Bioinformatics, Department of Biostatistics and Center of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
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12
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Welch RP, Lee C, Imbriano PM, Patil S, Weymouth TE, Smith RA, Scott LJ, Sartor MA. ChIP-Enrich: gene set enrichment testing for ChIP-seq data. Nucleic Acids Res 2014; 42:e105. [PMID: 24878920 PMCID: PMC4117744 DOI: 10.1093/nar/gku463] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Gene set enrichment testing can enhance the biological interpretation of ChIP-seq data. Here, we develop a method, ChIP-Enrich, for this analysis which empirically adjusts for gene locus length (the length of the gene body and its surrounding non-coding sequence). Adjustment for gene locus length is necessary because it is often positively associated with the presence of one or more peaks and because many biologically defined gene sets have an excess of genes with longer or shorter gene locus lengths. Unlike alternative methods, ChIP-Enrich can account for the wide range of gene locus length-to-peak presence relationships (observed in ENCODE ChIP-seq data sets). We show that ChIP-Enrich has a well-calibrated type I error rate using permuted ENCODE ChIP-seq data sets; in contrast, two commonly used gene set enrichment methods, Fisher's exact test and the binomial test implemented in Genomic Regions Enrichment of Annotations Tool (GREAT), can have highly inflated type I error rates and biases in ranking. We identify DNA-binding proteins, including CTCF, JunD and glucocorticoid receptor α (GRα), that show different enrichment patterns for peaks closer to versus further from transcription start sites. We also identify known and potential new biological functions of GRα. ChIP-Enrich is available as a web interface (http://chip-enrich.med.umich.edu) and Bioconductor package.
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Affiliation(s)
- Ryan P Welch
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA Biostatistics Department, University of Michigan, Ann Arbor, MI 48109, USA
| | - Chee Lee
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Paul M Imbriano
- Biostatistics Department, University of Michigan, Ann Arbor, MI 48109, USA
| | - Snehal Patil
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Terry E Weymouth
- Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - R Alex Smith
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Laura J Scott
- Biostatistics Department, University of Michigan, Ann Arbor, MI 48109, USA Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Maureen A Sartor
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA Biostatistics Department, University of Michigan, Ann Arbor, MI 48109, USA Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
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13
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Scott RA, Lagou V, Welch RP, Wheeler E, Montasser ME, Luan J, Mägi R, Strawbridge RJ, Rehnberg E, Gustafsson S, Kanoni S, Rasmussen-Torvik LJ, Yengo L, Lecoeur C, Shungin D, Sanna S, Sidore C, Johnson PCD, Jukema JW, Johnson T, Mahajan A, Verweij N, Thorleifsson G, Hottenga JJ, Shah S, Smith AV, Sennblad B, Gieger C, Salo P, Perola M, Timpson NJ, Evans DM, Pourcain BS, Wu Y, Andrews JS, Hui J, Bielak LF, Zhao W, Horikoshi M, Navarro P, Isaacs A, O'Connell JR, Stirrups K, Vitart V, Hayward C, Esko T, Mihailov E, Fraser RM, Fall T, Voight BF, Raychaudhuri S, Chen H, Lindgren CM, Morris AP, Rayner NW, Robertson N, Rybin D, Liu CT, Beckmann JS, Willems SM, Chines PS, Jackson AU, Kang HM, Stringham HM, Song K, Tanaka T, Peden JF, Goel A, Hicks AA, An P, Müller-Nurasyid M, Franco-Cereceda A, Folkersen L, Marullo L, Jansen H, Oldehinkel AJ, Bruinenberg M, Pankow JS, North KE, Forouhi NG, Loos RJF, Edkins S, Varga TV, Hallmans G, Oksa H, Antonella M, Nagaraja R, Trompet S, Ford I, Bakker SJL, Kong A, Kumari M, Gigante B, Herder C, Munroe PB, Caulfield M, Antti J, Mangino M, Small K, Miljkovic I, Liu Y, Atalay M, Kiess W, James AL, Rivadeneira F, Uitterlinden AG, Palmer CNA, Doney ASF, Willemsen G, Smit JH, Campbell S, Polasek O, Bonnycastle LL, Hercberg S, Dimitriou M, Bolton JL, Fowkes GR, Kovacs P, Lindström J, Zemunik T, Bandinelli S, Wild SH, Basart HV, Rathmann W, Grallert H, Maerz W, Kleber ME, Boehm BO, Peters A, Pramstaller PP, Province MA, Borecki IB, Hastie ND, Rudan I, Campbell H, Watkins H, Farrall M, Stumvoll M, Ferrucci L, Waterworth DM, Bergman RN, Collins FS, Tuomilehto J, Watanabe RM, de Geus EJC, Penninx BW, Hofman A, Oostra BA, Psaty BM, Vollenweider P, Wilson JF, Wright AF, Hovingh GK, Metspalu A, Uusitupa M, Magnusson PKE, Kyvik KO, Kaprio J, Price JF, Dedoussis GV, Deloukas P, Meneton P, Lind L, Boehnke M, Shuldiner AR, van Duijn CM, Morris AD, Toenjes A, Peyser PA, Beilby JP, Körner A, Kuusisto J, Laakso M, Bornstein SR, Schwarz PEH, Lakka TA, Rauramaa R, Adair LS, Smith GD, Spector TD, Illig T, de Faire U, Hamsten A, Gudnason V, Kivimaki M, Hingorani A, Keinanen-Kiukaanniemi SM, Saaristo TE, Boomsma DI, Stefansson K, van der Harst P, Dupuis J, Pedersen NL, Sattar N, Harris TB, Cucca F, Ripatti S, Salomaa V, Mohlke KL, Balkau B, Froguel P, Pouta A, Jarvelin MR, Wareham NJ, Bouatia-Naji N, McCarthy MI, Franks PW, Meigs JB, Teslovich TM, Florez JC, Langenberg C, Ingelsson E, Prokopenko I, Barroso I. Large-scale association analyses identify new loci influencing glycemic traits and provide insight into the underlying biological pathways. Nat Genet 2012; 44:991-1005. [PMID: 22885924 PMCID: PMC3433394 DOI: 10.1038/ng.2385] [Citation(s) in RCA: 623] [Impact Index Per Article: 51.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Accepted: 07/20/2012] [Indexed: 12/16/2022]
Abstract
Through genome-wide association meta-analyses of up to 133,010 individuals of European ancestry without diabetes, including individuals newly genotyped using the Metabochip, we have increased the number of confirmed loci influencing glycemic traits to 53, of which 33 also increase type 2 diabetes risk (q < 0.05). Loci influencing fasting insulin concentration showed association with lipid levels and fat distribution, suggesting impact on insulin resistance. Gene-based analyses identified further biologically plausible loci, suggesting that additional loci beyond those reaching genome-wide significance are likely to represent real associations. This conclusion is supported by an excess of directionally consistent and nominally significant signals between discovery and follow-up studies. Functional analysis of these newly discovered loci will further improve our understanding of glycemic control.
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Affiliation(s)
- Robert A Scott
- Medical Research Council Epidemiology Unit, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, UK
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Palmer ND, McDonough CW, Hicks PJ, Roh BH, Wing MR, An SS, Hester JM, Cooke JN, Bostrom MA, Rudock ME, Talbert ME, Lewis JP, Ferrara A, Lu L, Ziegler JT, Sale MM, Divers J, Shriner D, Adeyemo A, Rotimi CN, Ng MCY, Langefeld CD, Freedman BI, Bowden DW, Voight BF, Scott LJ, Steinthorsdottir V, Morris AP, Dina C, Welch RP, Zeggini E, Huth C, Aulchenko YS, Thorleifsson G, McCulloch LJ, Ferreira T, Grallert H, Amin N, Wu G, Willer CJ, Raychaudhuri S, McCarroll SA, Langenberg C, Hofmann OM, Dupuis J, Qi L, Segrè AV, van Hoek M, Navarro P, Ardlie K, Balkau B, Benediktsson R, Bennett AJ, Blagieva R, Boerwinkle E, Bonnycastle LL, Boström KB, Bravenboer B, Bumpstead S, Burtt NP, Charpentier G, Chines PS, Cornelis M, Couper DJ, Crawford G, Doney ASF, Elliott KS, Elliott AL, Erdos MR, Fox CS, Franklin CS, Ganser M, Gieger C, Grarup N, Green T, Griffin S, Groves CJ, Guiducci C, Hadjadj S, Hassanali N, Herder C, Isomaa B, Jackson AU, Johnson PRV, Jørgensen T, Kao WHL, Klopp N, Kong A, Kraft P, Kuusisto J, Lauritzen T, Li M, Lieverse A, Lindgren CM, Lyssenko V, Marre M, Meitinger T, Midthjell K, Morken MA, Narisu N, Nilsson P, Owen KR, Payne F, Perry JRB, Petersen AK, Platou C, Proença C, Prokopenko I, Rathmann W, Rayner NW, Robertson NR, Rocheleau G, Roden M, Sampson MJ, Saxena R, Shields BM, Shrader P, Sigurdsson G, Sparsø T, Strassburger K, Stringham HM, Sun Q, Swift AJ, Thorand B, Tichet J, Tuomi T, van Dam RM, van Haeften TW, van Herpt T, van Vliet-Ostaptchouk JV, Walters GB, Weedon MN, Wijmenga C, Witteman J, Bergman RN, Cauchi S, Collins FS, Gloyn AL, Gyllensten U, Hansen T, Hide WA, Hitman GA, Hofman A, Hunter DJ, Hveem K, Laakso M, Mohlke KL, Morris AD, Palmer CNA, Pramstaller PP, Rudan I, Sijbrands E, Stein LD, Tuomilehto J, Uitterlinden A, Walker M, Wareham NJ, Watanabe RM, Abecasis GR, Boehm BO, Campbell H, Daly MJ, Hattersley AT, Hu FB, Meigs JB, Pankow JS, Pedersen O, Wichmann HE, Barroso I, Florez JC, Frayling TM, Groop L, Sladek R, Thorsteinsdottir U, Wilson JF, Illig T, Froguel P, van Duijn CM, Stefansson K, Altshuler D, Boehnke M, McCarthy MI, Soranzo N, Wheeler E, Glazer NL, Bouatia-Naji N, Mägi R, Randall J, Johnson T, Elliott P, Rybin D, Henneman P, Dehghan A, Hottenga JJ, Song K, Goel A, Egan JM, Lajunen T, Doney A, Kanoni S, Cavalcanti-Proença C, Kumari M, Timpson NJ, Zabena C, Ingelsson E, An P, O'Connell J, Luan J, Elliott A, McCarroll SA, Roccasecca RM, Pattou F, Sethupathy P, Ariyurek Y, Barter P, Beilby JP, Ben-Shlomo Y, Bergmann S, Bochud M, Bonnefond A, Borch-Johnsen K, Böttcher Y, Brunner E, Bumpstead SJ, Chen YDI, Chines P, Clarke R, Coin LJM, Cooper MN, Crisponi L, Day INM, de Geus EJC, Delplanque J, Fedson AC, Fischer-Rosinsky A, Forouhi NG, Frants R, Franzosi MG, Galan P, Goodarzi MO, Graessler J, Grundy S, Gwilliam R, Hallmans G, Hammond N, Han X, Hartikainen AL, Hayward C, Heath SC, Hercberg S, Hicks AA, Hillman DR, Hingorani AD, Hui J, Hung J, Jula A, Kaakinen M, Kaprio J, Kesaniemi YA, Kivimaki M, Knight B, Koskinen S, Kovacs P, Kyvik KO, Lathrop GM, Lawlor DA, Le Bacquer O, Lecoeur C, Li Y, Mahley R, Mangino M, Manning AK, Martínez-Larrad MT, McAteer JB, McPherson R, Meisinger C, Melzer D, Meyre D, Mitchell BD, Mukherjee S, Naitza S, Neville MJ, Oostra BA, Orrù M, Pakyz R, Paolisso G, Pattaro C, Pearson D, Peden JF, Pedersen NL, Perola M, Pfeiffer AFH, Pichler I, Polasek O, Posthuma D, Potter SC, Pouta A, Province MA, Psaty BM, Rayner NW, Rice K, Ripatti S, Rivadeneira F, Rolandsson O, Sandbaek A, Sandhu M, Sanna S, Sayer AA, Scheet P, Seedorf U, Sharp SJ, Shields B, Sijbrands EJG, Silveira A, Simpson L, Singleton A, Smith NL, Sovio U, Swift A, Syddall H, Syvänen AC, Tanaka T, Tönjes A, Uitterlinden AG, van Dijk KW, Varma D, Visvikis-Siest S, Vitart V, Vogelzangs N, Waeber G, Wagner PJ, Walley A, Ward KL, Watkins H, Wild SH, Willemsen G, Witteman JCM, Yarnell JWG, Zelenika D, Zethelius B, Zhai G, Zhao JH, Zillikens MC, Borecki IB, Loos RJF, Meneton P, Magnusson PKE, Nathan DM, Williams GH, Silander K, Salomaa V, Smith GD, Bornstein SR, Schwarz P, Spranger J, Karpe F, Shuldiner AR, Cooper C, Dedoussis GV, Serrano-Ríos M, Lind L, Palmer LJ, Franks PW, Ebrahim S, Marmot M, Kao WHL, Pramstaller PP, Wright AF, Stumvoll M, Hamsten A, Buchanan TA, Valle TT, Rotter JI, Siscovick DS, Penninx BWJH, Boomsma DI, Deloukas P, Spector TD, Ferrucci L, Cao A, Scuteri A, Schlessinger D, Uda M, Ruokonen A, Jarvelin MR, Waterworth DM, Vollenweider P, Peltonen L, Mooser V, Sladek R. A genome-wide association search for type 2 diabetes genes in African Americans. PLoS One 2012; 7:e29202. [PMID: 22238593 PMCID: PMC3251563 DOI: 10.1371/journal.pone.0029202] [Citation(s) in RCA: 137] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Accepted: 11/22/2011] [Indexed: 12/16/2022] Open
Abstract
African Americans are disproportionately affected by type 2 diabetes (T2DM) yet few studies have examined T2DM using genome-wide association approaches in this ethnicity. The aim of this study was to identify genes associated with T2DM in the African American population. We performed a Genome Wide Association Study (GWAS) using the Affymetrix 6.0 array in 965 African-American cases with T2DM and end-stage renal disease (T2DM-ESRD) and 1029 population-based controls. The most significant SNPs (n = 550 independent loci) were genotyped in a replication cohort and 122 SNPs (n = 98 independent loci) were further tested through genotyping three additional validation cohorts followed by meta-analysis in all five cohorts totaling 3,132 cases and 3,317 controls. Twelve SNPs had evidence of association in the GWAS (P<0.0071), were directionally consistent in the Replication cohort and were associated with T2DM in subjects without nephropathy (P<0.05). Meta-analysis in all cases and controls revealed a single SNP reaching genome-wide significance (P<2.5×10(-8)). SNP rs7560163 (P = 7.0×10(-9), OR (95% CI) = 0.75 (0.67-0.84)) is located intergenically between RND3 and RBM43. Four additional loci (rs7542900, rs4659485, rs2722769 and rs7107217) were associated with T2DM (P<0.05) and reached more nominal levels of significance (P<2.5×10(-5)) in the overall analysis and may represent novel loci that contribute to T2DM. We have identified novel T2DM-susceptibility variants in the African-American population. Notably, T2DM risk was associated with the major allele and implies an interesting genetic architecture in this population. These results suggest that multiple loci underlie T2DM susceptibility in the African-American population and that these loci are distinct from those identified in other ethnic populations.
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Affiliation(s)
- Nicholette D Palmer
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, North Carolina, United States of America.
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Voight BF, Scott LJ, Steinthorsdottir V, Morris AP, Dina C, Welch RP, Zeggini E, Huth C, Aulchenko YS, Thorleifsson G, McCulloch LJ, Ferreira T, Grallert H, Amin N, Wu G, Willer CJ, Raychaudhuri S, McCarroll SA, Langenberg C, Hofmann OM, Dupuis J, Qi L, Segrè AV, van Hoek M, Navarro P, Ardlie K, Balkau B, Benediktsson R, Bennett AJ, Blagieva R, Boerwinkle E, Bonnycastle LL, Boström KB, Bravenboer B, Bumpstead S, Burtt NP, Charpentier G, Chines PS, Cornelis M, Couper DJ, Crawford G, Doney ASF, Elliott KS, Elliott AL, Erdos MR, Fox CS, Franklin CS, Ganser M, Gieger C, Grarup N, Green T, Griffin S, Groves CJ, Guiducci C, Hadjadj S, Hassanali N, Herder C, Isomaa B, Jackson AU, Johnson PRV, Jørgensen T, Kao WHL, Klopp N, Kong A, Kraft P, Kuusisto J, Lauritzen T, Li M, Lieverse A, Lindgren CM, Lyssenko V, Marre M, Meitinger T, Midthjell K, Morken MA, Narisu N, Nilsson P, Owen KR, Payne F, Perry JRB, Petersen AK, Platou C, Proença C, Prokopenko I, Rathmann W, Rayner NW, Robertson NR, Rocheleau G, Roden M, Sampson MJ, Saxena R, Shields BM, Shrader P, Sigurdsson G, Sparsø T, Strassburger K, Stringham HM, Sun Q, Swift AJ, Thorand B, Tichet J, Tuomi T, van Dam RM, van Haeften TW, van Herpt T, van Vliet-Ostaptchouk JV, Walters GB, Weedon MN, Wijmenga C, Witteman J, Bergman RN, Cauchi S, Collins FS, Gloyn AL, Gyllensten U, Hansen T, Hide WA, Hitman GA, Hofman A, Hunter DJ, Hveem K, Laakso M, Mohlke KL, Morris AD, Palmer CNA, Pramstaller PP, Rudan I, Sijbrands E, Stein LD, Tuomilehto J, Uitterlinden A, Walker M, Wareham NJ, Watanabe RM, Abecasis GR, Boehm BO, Campbell H, Daly MJ, Hattersley AT, Hu FB, Meigs JB, Pankow JS, Pedersen O, Wichmann HE, Barroso I, Florez JC, Frayling TM, Groop L, Sladek R, Thorsteinsdottir U, Wilson JF, Illig T, Froguel P, van Duijn CM, Stefansson K, Altshuler D, Boehnke M, McCarthy MI. Erratum: Corrigendum: Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis. Nat Genet 2011. [DOI: 10.1038/ng0411-388b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Voight BF, Scott LJ, Steinthorsdottir V, Morris AP, Dina C, Welch RP, Zeggini E, Huth C, Aulchenko YS, Thorleifsson G, McCulloch LJ, Ferreira T, Grallert H, Amin N, Wu G, Willer CJ, Raychaudhuri S, McCarroll SA, Langenberg C, Hofmann OM, Dupuis J, Qi L, Segrè AV, van Hoek M, Navarro P, Ardlie K, Balkau B, Benediktsson R, Bennett AJ, Blagieva R, Boerwinkle E, Bonnycastle LL, Bengtsson Boström K, Bravenboer B, Bumpstead S, Burtt NP, Charpentier G, Chines PS, Cornelis M, Couper DJ, Crawford G, Doney ASF, Elliott KS, Elliott AL, Erdos MR, Fox CS, Franklin CS, Ganser M, Gieger C, Grarup N, Green T, Griffin S, Groves CJ, Guiducci C, Hadjadj S, Hassanali N, Herder C, Isomaa B, Jackson AU, Johnson PRV, Jørgensen T, Kao WHL, Klopp N, Kong A, Kraft P, Kuusisto J, Lauritzen T, Li M, Lieverse A, Lindgren CM, Lyssenko V, Marre M, Meitinger T, Midthjell K, Morken MA, Narisu N, Nilsson P, Owen KR, Payne F, Perry JRB, Petersen AK, Platou C, Proença C, Prokopenko I, Rathmann W, Rayner NW, Robertson NR, Rocheleau G, Roden M, Sampson MJ, Saxena R, Shields BM, Shrader P, Sigurdsson G, Sparsø T, Strassburger K, Stringham HM, Sun Q, Swift AJ, Thorand B, Tichet J, Tuomi T, van Dam RM, van Haeften TW, van Herpt T, van Vliet-Ostaptchouk JV, Walters GB, Weedon MN, Wijmenga C, Witteman J, Bergman RN, Cauchi S, Collins FS, Gloyn AL, Gyllensten U, Hansen T, Hide WA, Hitman GA, Hofman A, Hunter DJ, Hveem K, Laakso M, Mohlke KL, Morris AD, Palmer CNA, Pramstaller PP, Rudan I, Sijbrands E, Stein LD, Tuomilehto J, Uitterlinden A, Walker M, Wareham NJ, Watanabe RM, Abecasis GR, Boehm BO, Campbell H, Daly MJ, Hattersley AT, Hu FB, Meigs JB, Pankow JS, Pedersen O, Wichmann HE, Barroso I, Florez JC, Frayling TM, Groop L, Sladek R, Thorsteinsdottir U, Wilson JF, Illig T, Froguel P, van Duijn CM, Stefansson K, Altshuler D, Boehnke M, McCarthy MI. Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis. Nat Genet 2010; 42:579-89. [PMID: 20581827 DOI: 10.1038/ng.609] [Citation(s) in RCA: 1338] [Impact Index Per Article: 95.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2010] [Accepted: 05/26/2010] [Indexed: 12/11/2022]
Abstract
By combining genome-wide association data from 8,130 individuals with type 2 diabetes (T2D) and 38,987 controls of European descent and following up previously unidentified meta-analysis signals in a further 34,412 cases and 59,925 controls, we identified 12 new T2D association signals with combined P<5x10(-8). These include a second independent signal at the KCNQ1 locus; the first report, to our knowledge, of an X-chromosomal association (near DUSP9); and a further instance of overlap between loci implicated in monogenic and multifactorial forms of diabetes (at HNF1A). The identified loci affect both beta-cell function and insulin action, and, overall, T2D association signals show evidence of enrichment for genes involved in cell cycle regulation. We also show that a high proportion of T2D susceptibility loci harbor independent association signals influencing apparently unrelated complex traits.
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Affiliation(s)
- Benjamin F Voight
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
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Pruim RJ, Welch RP, Sanna S, Teslovich TM, Chines PS, Gliedt TP, Boehnke M, Abecasis GR, Willer CJ. LocusZoom: regional visualization of genome-wide association scan results. Bioinformatics 2010; 26:2336-7. [PMID: 20634204 PMCID: PMC2935401 DOI: 10.1093/bioinformatics/btq419] [Citation(s) in RCA: 2007] [Impact Index Per Article: 143.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Summary: Genome-wide association studies (GWAS) have revealed hundreds of loci associated with common human genetic diseases and traits. We have developed a web-based plotting tool that provides fast visual display of GWAS results in a publication-ready format. LocusZoom visually displays regional information such as the strength and extent of the association signal relative to genomic position, local linkage disequilibrium (LD) and recombination patterns and the positions of genes in the region. Availability: LocusZoom can be accessed from a web interface at http://csg.sph.umich.edu/locuszoom. Users may generate a single plot using a web form, or many plots using batch mode. The software utilizes LD information from HapMap Phase II (CEU, YRI and JPT+CHB) or 1000 Genomes (CEU) and gene information from the UCSC browser, and will accept SNP identifiers in dbSNP or 1000 Genomes format. Single plots are generated in ∼20 s. Source code and associated databases are available for download and local installation, and full documentation is available online. Contact:cristen@umich.edu
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Affiliation(s)
- Randall J Pruim
- Department of Mathematics and Statistics, Calvin College, Grand Rapids, MI 49546, USA
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Abstract
Although technology exists to sustain vital functions of almost any patient, not every pulse-less patient is a candidate for resuscitation. Criteria needs to be developed to guide health care professionals in identifying DNR situations and teaching families about DNR options. The first step is to identify characteristics that are related to current DNR selection, so prescriptive criteria can be developed to aid in DNR decisions in the future. This article presents a descriptive study of characteristics associated with DNR statistics for pediatric ICU patients.
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Biggs PA, Middleton JE, Welch RP. Interference in urine oxalate assay (sigma diagnostics oxalate oxidase method) from homogentisic acid in alkaptonuria. Clin Chem 1986. [DOI: 10.1093/clinchem/32.8.1598a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Biggs PA, Middleton JE, Welch RP. Interference in urine oxalate assay (sigma diagnostics oxalate oxidase method) from homogentisic acid in alkaptonuria. Clin Chem 1986; 32:1598. [PMID: 3731474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Chrzanowski TH, Crotty RD, Hubbard JG, Welch RP. Applicability of the fluorescein diacetate method of detecting active bacteria in freshwater. Microb Ecol 1984; 10:179-85. [PMID: 24221097 DOI: 10.1007/bf02011424] [Citation(s) in RCA: 60] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Fluorescein diacetate (FDA) hydrolysis was evaluated as a means to detect actively metabolizing bacteria in freshwater. Fluorescein diacetate, a nonfluorescent derivative of fluorescein, can be transported across cell membranes and deacetylated by nonspecific esterases. Resultant fluorescein accumulates within cells and allows direct visualization by epifluorescent microscopy. Application of FDA to a variety of freshwater habitats yielded estimates of active cells ranging from 6-24% of the total population. These estimates were 49-61% lower than estimates of active cells obtained from measures of electron transport activity. The difference was attributed to low permeability of the fluorogen through the outer membrane of heterotrophic gram-negative cells. Data suggest that FDA hydrolysis as a means of detecting active bacteria may be limited to environments rich in eucaryotes and gram-positive cells.
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Affiliation(s)
- T H Chrzanowski
- Department of Biology, The University of Texas at Arlington, 76019, Arlington, Texas, USA
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Weeks B, Welch RP. Zuckerman overtaken. West J Med 1978. [DOI: 10.1136/bmj.2.6150.1495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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