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Originally published in Science Express on 26 April 2007
Science 1 June 2007:
Vol. 316. no. 5829, pp. 1331 - 1336
DOI: 10.1126/science.1142358
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Genome-Wide Association Analysis Identifies Loci for Type 2 Diabetes and Triglyceride Levels

Diabetes Genetics Initiative of Broad Institute of Harvard and MIT, Lund University, and Novartis Institutes of BioMedical Research: *{dagger} Richa Saxena,1,2,3,4,5,6 Benjamin F. Voight,1,2,3,5 Valeriya Lyssenko,7 Noël P. Burtt,1 Paul I. W. de Bakker,1,2,3,4,5,6 Hong Chen,8 Jeffrey J. Roix,8 Sekar Kathiresan,1,3,5 Joel N. Hirschhorn,1,6,9,10,11 Mark J. Daly,1,2,3,5 Thomas E. Hughes,8 Leif Groop,7,12 David Altshuler,1,2,3,4,5,6 Peter Almgren,7 Jose C. Florez,1,2,3,4,5,6 Joanne Meyer,8 Kristin Ardlie,1 Kristina Bengtsson Boström,13 Bo Isomaa,14,15 Guillaume Lettre,1,6,9,10,11 Ulf Lindblad,16 Helen N. Lyon,1,6,9,10,11 Olle Melander,7 Christopher Newton-Cheh,1,2,3,5 Peter Nilsson,17 Marju Orho-Melander,7 Lennart Råstam,16 Elizabeth K. Speliotes,1,3,6,9,10,11 Marja-Riitta Taskinen,12 Tiinamaija Tuomi,12,15 Candace Guiducci,1 Anna Berglund,7 Joyce Carlson,18 Lauren Gianniny,1 Rachel Hackett,1 Liselotte Hall,18 Johan Holmkvist,7 Esa Laurila,7 Marketa Sjögren,7 Maria Sterner,18 Aarti Surti,1 Margareta Svensson,7 Malin Svensson,7 Ryan Tewhey,1 Brendan Blumenstiel,1 Melissa Parkin,1 Matthew DeFelice,1 Rachel Barry,1 Wendy Brodeur,1 Jody Camarata,1 Nancy Chia,1 Mary Fava,1 John Gibbons,1 Bob Handsaker,1 Claire Healy,1 Kieu Nguyen,1 Casey Gates,1 Carrie Sougnez,1 Diane Gage,1 Marcia Nizzari,1 Stacey B. Gabriel,1 Gung-Wei Chirn,8 Qicheng Ma,8 Hemang Parikh,7 Delwood Richardson,8 Darrell Ricke,8 Shaun Purcell1,2,19

New strategies for prevention and treatment of type 2 diabetes (T2D) require improved insight into disease etiology. We analyzed 386,731 common single-nucleotide polymorphisms (SNPs) in 1464 patients with T2D and 1467 matched controls, each characterized for measures of glucose metabolism, lipids, obesity, and blood pressure. With collaborators (FUSION and WTCCC/UKT2D), we identified and confirmed three loci associated with T2D—in a noncoding region near CDKN2A and CDKN2B, in an intron of IGF2BP2, and an intron of CDKAL1—and replicated associations near HHEX and in SLC30A8 found by a recent whole-genome association study. We identified and confirmed association of a SNP in an intron of glucokinase regulatory protein (GCKR) with serum triglycerides. The discovery of associated variants in unsuspected genes and outside coding regions illustrates the ability of genome-wide association studies to provide potentially important clues to the pathogenesis of common diseases.

1 Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA 02142, USA.
2 Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA.
3 Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.
4 Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA.
5 Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.
6 Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
7 Department of Clinical Sciences, Diabetes and Endocrinology Research Unit, University Hospital Malmö, Lund University, Malmö, Sweden.
8 Diabetes and Metabolism Disease Area, Novartis Institutes for BioMedical Research, 100 Technology Square, Cambridge, MA 02139, USA.
9 Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA.
10 Division of Endocrinology, Children’s Hospital, Boston, MA 02115, USA.
11 Division of Genetics, Children’s Hospital, Boston, MA 02115, USA.
12 Department of Medicine, Helsinki University Hospital, University of Helsinki, Helsinki, Finland.
13 Skaraborg Institute, Skövde, Sweden.
14 Malmska Municipal Health Center and Hospital, Jakobstad, Finland.
15 Folkhälsan Research Center, Helsinki, Finland.
16 Department of Clinical Sciences, Community Medicine Research Unit, University Hospital Malmö, Lund University, Malmö, Sweden.
17 Department of Clinical Sciences, Medicine Research Unit, University Hospital Malmö, Lund University, Malmö, Sweden.
18 Clinical Chemistry, University Hospital Malmö, Lund University, Malmö, Sweden.
19 Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA.

{dagger} All authors with their contributions and affiliations appear at the end of this paper.

* To whom correspondence should be addressed: David Altshuler, Leif Groop, Thomas E. Hughes. E-mail: altshuler{at}molbio.mgh.harvard.edu (D.A.); leif.groop{at}med.lu.se (L.G.); thomase.hughes{at}novartis.com (T.E.H.)

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J. F. Thompson, C. L. Hyde, L. S. Wood, S. A. Paciga, D. A. Hinds, D. R. Cox, G. K. Hovingh, and J. J.P. Kastelein (2009)
Circ Cardiovasc Genet 2, 173-181
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TCF7L2 Regulates Late Events in Insulin Secretion From Pancreatic Islet {beta}-Cells.
G. da Silva Xavier, M. K. Loder, A. McDonald, A. I. Tarasov, R. Carzaniga, K. Kronenberger, S. Barg, and G. A. Rutter (2009)
Diabetes 58, 894-905
   Abstract »    Full Text »    PDF »
Clinical risk factors, DNA variants, and the development of type 2 diabetes..
K.M. V. Narayan, M. B. Weber, J. Gulcher, K. Stefansson, V. Lyssenko, P. Nilsson, and L. Groop (2009)
N. Engl. J. Med. 360, 1360
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Genetic Variations in Sex Steroid-Related Genes as Predictors of Serum Estrogen Levels in Men.
A. L. Eriksson, M. Lorentzon, L. Vandenput, F. Labrie, M. Lindersson, A.-C. Syvanen, E. S. Orwoll, S. R. Cummings, J. M. Zmuda, O. Ljunggren, et al. (2009)
J. Clin. Endocrinol. Metab. 94, 1033-1041
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Genetic association of the activin A receptor gene (ACVR2A) and pre-eclampsia.
E. Fitzpatrick, M.P. Johnson, T.D. Dyer, S. Forrest, K. Elliott, J. Blangero, S.P. Brennecke, and E.K. Moses (2009)
Mol. Hum. Reprod. 15, 195-204
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The genomic architecture of segmental duplications and associated copy number variants in dogs.
T. J. Nicholas, Z. Cheng, M. Ventura, K. Mealey, E. E. Eichler, and J. M. Akey (2009)
Genome Res. 19, 491-499
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Interaction Effect of Genetic Polymorphisms in Glucokinase (GCK) and Glucokinase Regulatory Protein (GCKR) on Metabolic Traits in Healthy Chinese Adults and Adolescents.
C. H.T. Tam, R. C.W. Ma, W. Y. So, Y. Wang, V. K.L. Lam, S. Germer, M. Martin, J. C.N. Chan, and M. C.Y. Ng (2009)
Diabetes 58, 765-769
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Diabetes: Vascular or Neurodegenerative: An Epidemiologic Perspective.
L. J. Launer (2009)
Stroke 40, S53-S55
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Whole Genome Approaches in Ischemic Stroke.
J. F. Meschia (2009)
Stroke 40, S61-S63
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ATOM: a powerful gene-based association test by combining optimally weighted markers.
M. Li, K. Wang, S. F. A. Grant, H. Hakonarson, and C. Li (2009)
Bioinformatics 25, 497-503
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Transient ciliogenesis involving Bardet-Biedl syndrome proteins is a fundamental characteristic of adipogenic differentiation.
V. Marion, C. Stoetzel, D. Schlicht, N. Messaddeq, M. Koch, E. Flori, J. M. Danse, J.-L. Mandel, and H. Dollfus (2009)
PNAS 106, 1820-1825
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STrengthening the REporting of Genetic Association Studies (STREGA): An Extension of the STROBE Statement.
J. Little, J. P.T. Higgins, J. P.A. Ioannidis, D. Moher, F. Gagnon, E. von Elm, M. J. Khoury, B. Cohen, G. Davey-Smith, J. Grimshaw, et al. (2009)
Ann Intern Med 150, 206-215
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Genome-Wide Association Studies for Atherosclerotic Vascular Disease and Its Risk Factors.
K. Ding and I. J. Kullo (2009)
Circ Cardiovasc Genet 2, 63-72
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Association of Regions on Chromosomes 6 and 7 With Blood Pressure in Nigerian Families.
B. O. Tayo, A. Luke, X. Zhu, A. Adeyemo, and R. S. Cooper (2009)
Circ Cardiovasc Genet 2, 38-45
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Size matters: just how big is BIG?: Quantifying realistic sample size requirements for human genome epidemiology.
P. R Burton, A. L Hansell, I. Fortier, T. A Manolio, M. J Khoury, J. Little, and P. Elliott (2009)
Int. J. Epidemiol. 38, 263-273
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Association Analysis of Variation in/Near FTO, CDKAL1, SLC30A8, HHEX, EXT2, IGF2BP2, LOC387761, and CDKN2B With Type 2 Diabetes and Related Quantitative Traits in Pima Indians.
R. Rong, R. L. Hanson, D. Ortiz, C. Wiedrich, S. Kobes, W. C. Knowler, C. Bogardus, and L. J. Baier (2009)
Diabetes 58, 478-488
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Replication Study of Candidate Genes Associated With Type 2 Diabetes Based On Genome-Wide Screening.
Y. Tabara, H. Osawa, R. Kawamoto, H. Onuma, I. Shimizu, T. Miki, K. Kohara, and H. Makino (2009)
Diabetes 58, 493-498
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Adiposity-Related Heterogeneity in Patterns of Type 2 Diabetes Susceptibility Observed in Genome-Wide Association Data.
N. J. Timpson, C. M. Lindgren, M. N. Weedon, J. Randall, W. H. Ouwehand, D. P. Strachan, N. W. Rayner, M. Walker, G. A. Hitman, A. S.F. Doney, et al. (2009)
Diabetes 58, 505-510
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Genetic Epidemiology in Aging Research.
M. D. Fallin and A. Matteini (2009)
J Gerontol A Biol Sci Med Sci
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Cardiovascular Disease Risk Prediction With and Without Knowledge of Genetic Variation at Chromosome 9p21.3.
N. P. Paynter, D. I. Chasman, J. E. Buring, D. Shiffman, N. R. Cook, and P. M. Ridker (2009)
Ann Intern Med 150, 65-72
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Identification of a common variant at the NOS1AP locus strongly associated to QT-interval duration.
M. Eijgelsheim, A. L.H.J. Aarnoudse, F. Rivadeneira, J. A. Kors, J. C. M. Witteman, A. Hofman, C. M. van Duijn, A. G. Uitterlinden, and B. H.C. Stricker (2009)
Hum. Mol. Genet. 18, 347-357
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IFIH1 polymorphisms are significantly associated with type 1 diabetes and IFIH1 gene expression in peripheral blood mononuclear cells.
S. Liu, H. Wang, Y. Jin, R. Podolsky, M. P. L. Reddy, J. Pedersen, B. Bode, J. Reed, D. Steed, S. Anderson, et al. (2009)
Hum. Mol. Genet. 18, 358-365
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Gene-Environment Interaction in Genome-Wide Association Studies.
C. E. Murcray, J. P. Lewinger, and W. J. Gauderman (2009)
Am. J. Epidemiol. 169, 219-226
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Stem Cells Use Distinct Self-renewal Programs at Different Ages.
B.P. Levi and S.J. Morrison (2009)
Cold Spring Harb Symp Quant Biol
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From the Cover: Whole-genome association study identifies STK39 as a hypertension susceptibility gene.
Y. Wang, J. R. O'Connell, P. F. McArdle, J. B. Wade, S. E. Dorff, S. J. Shah, X. Shi, L. Pan, E. Rampersaud, H. Shen, et al. (2009)
PNAS 106, 226-231
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Genetic basis of HDL variation in 129/SvImJ and C57BL/6J mice: importance of testing candidate genes in targeted mutant mice.
Z. Su, X. Wang, S.-W. Tsaih, A. Zhang, A. Cox, S. Sheehan, and B. Paigen (2009)
J. Lipid Res. 50, 116-125
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