Genome-wide association study in individuals of South Asian ancestry identifies six new type 2 diabetes susceptibility loci

Nature Genetics

Volumn 43, Issue 10, 2011, Pages 984-989

  Kooner, Jaspal S ^a,b,c   Saleheen, Danish ^d,e   Sim, Xueling ^f   Sehmi, Joban ^a,b   Zhang, Weihua ^g   Frossard, Philippe ^d   Been, Latonya F ^h   Chia, Kee Seng ^f   Dimas, Antigone S ^i,j   Hassanali, Neelam ^k   Jafar, Tazeen ^l,m   Jowett, Jeremy B M ⁿ   Li, Xinzhong ^a   Radha, Venkatesan ^o   Rees, Simon D ^p,q   Takeuchi, Fumihiko ^r   Young, Robin ^e   Aung, Tin ^f,s   Basit, Abdul ^t   Chidambaram, Manickam ^o   Das, Debashish ^b   Grundberg, Elin ^u   Hedman, Åsa K ^j   Hydrie, Zafar I ^t   Islam, Muhammed ^l   Khor, Chiea Chuen ^f,s,v   Kowlessur, Sudhir ^w   Kristensen, Malene M ⁿ   Liju, Samuel ^o   Lim, Wei Yen ^f   Matthews, David R ^k   Liu, Jianjun ^v   Morris, Andrew P ^j   Nica, Alexandra C ⁱ   Pinidiyapathirage, Janani M ^x   Prokopenko, Inga ^j   Rasheed, Asif ^d   Samuel, Maria ^d   Shah, Nabi ^d   Shera, A Samad ^y   Small, Kerrin S ^u,z   Suo, Chen ^f   Wickremasinghe, Ananda R ^x   Wong, Tien Yin ^f,s,aa   Yang, Mingyu ^ab   Zhang, Fan ^ab   Abecasis, Goncalo R ^ac   Barnett, Anthony H ^p,q   Caulfield, Mark ^ad   Deloukas, Panos ^z   Frayling, Timothy M ^ae   Froguel, Philippe ^af   Kato, Norihiro ^r   Katulanda, Prasad ^k,ag   Kelly, M Ann ^p,q   Liang, Junbin ^ab   Mohan, Viswanathan ^o,ah   Sanghera, Dharambir K ^h   Scott, James ^a   Seielstad, Mark ^ai   Zimmet, Paul Z ⁿ   Elliott, Paul ^g,aj   Teo, Yik Ying ^f,v   McCarthy, Mark I ^j,k,ak   Danesh, John ^e   Tai, E Shyong ^f   Chambers, John C ^b,c,g   more..

^a NATIONAL HEART AND LUNG INSTITUTE   (United Kingdom)

^b EALING HOSPITAL NHS TRUST   (United Kingdom)

^c IMPERIAL COLLEGE HEALTHCARE NHS TRUST   (United Kingdom)

^d Center for Non Communicable Diseases Pakistan   (Pakistan)

^e UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^f NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^g IMPERIAL COLLEGE LONDON   (United Kingdom)

^h UNIVERSITY OF OKLAHOMA COLLEGE OF MEDICINE   (United States)

ⁱ UNIVERSITY OF GENEVA MEDICAL SCHOOL   (Switzerland)

^j UNIVERSITY OF OXFORD   (United Kingdom)

^k UNIVERSITY OF OXFORD   (United Kingdom)

^l AGA KHAN UNIVERSITY   (Pakistan)

^m AGA KHAN UNIVERSITY HOSPITAL   (Pakistan)

ⁿ BAKER IDI HEART AND DIABETES INSTITUTE   (Australia)

^o INDIAN COUNCIL OF MEDICAL RESEARCH   (India)

^p UNIVERSITY OF BIRMINGHAM   (United Kingdom)

^q UNIVERSITY HOSPITALS BIRMINGHAM NHS FOUNDATION TRUST   (United Kingdom)

^r NATIONAL CENTER FOR GLOBAL HEALTH AND MEDICINE   (Japan)

^s SINGAPORE EYE RESEARCH INSTITUTE   (Singapore)

^t BAQAI MEDICAL UNIVERSITY   (Pakistan)

^u KING'S COLLEGE LONDON   (United Kingdom)

^v GENOME INSTITUTE OF SINGAPORE   (Singapore)

^w Ministry of Health   (Mauritius)

^x UNIVERSITY OF KELANIYA   (Sri Lanka)

^y Diabetic Association Pakistan   (Pakistan)

^z WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^aa UNIVERSITY OF MELBOURNE   (Australia)

^ab BGI SHENZHEN   (China)

^ac UNIVERSITY OF MICHIGAN   (United States)

^ad QUEEN MARY UNIVERSITY OF LONDON   (United Kingdom)

^ae UNIVERSITY OF EXETER   (United Kingdom)

^af HAMMERSMITH HOSPITAL   (United Kingdom)

^ag UNIVERSITY OF COLOMBO   (Sri Lanka)

^ah Dr Mohan's Diabetes Specialties Centre   (India)

^ai UNIVERSITY OF CALIFORNIA   (United States)

^aj MEDICAL RESEARCH COUNCIL   (United Kingdom)

^ak NIHR OXFORD BIOMEDICAL RESEARCH CENTRE   (United Kingdom)

more..

Author keywords

[No Author keywords available]

Indexed keywords

ADULT; ARTICLE; CLINICAL ARTICLE; CONTROLLED STUDY; FEMALE; GENE LOCUS; GENE REPLICATION; GENETIC ASSOCIATION; GENETIC IDENTIFICATION; GENETIC PREDISPOSITION; GENETIC SUSCEPTIBILITY; GENOME ANALYSIS; HUMAN; INSULIN SENSITIVITY; MALE; NON INSULIN DEPENDENT DIABETES MELLITUS; PAKISTAN; PANCREAS ISLET BETA CELL; POPULATION GENETICS; PRIORITY JOURNAL; SINGAPORE; SINGLE NUCLEOTIDE POLYMORPHISM; SOUTH ASIA; UNITED KINGDOM;

ASIAN CONTINENTAL ANCESTRY GROUP; CASE-CONTROL STUDIES; DIABETES MELLITUS, TYPE 2; FEMALE; GENE EXPRESSION REGULATION; GENETIC PREDISPOSITION TO DISEASE; GENETICS, POPULATION; GENOME, HUMAN; GENOME-WIDE ASSOCIATION STUDY; HUMANS; LINKAGE DISEQUILIBRIUM; LONDON; MALE; PAKISTAN; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI; SINGAPORE;

EID: 80053385333     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng.921     Document Type: Article

References (57)

1. Chambers, J.C. et al. Plasma homocysteine concentrations and risk of coronary heart disease in UK Indian Asian and European men. Lancet 355, 523-527 (2000). (Pubitemid 30088671)
2. Ramachandran, A., Ma, R.C. & Snehalatha, C. Diabetes in Asia. Lancet 375, 408-418 (2010).
3. Shaw, J.E., Sicree, R.A. & Zimmet, P.Z. Global estimates of the prevalence of diabetes for 2010 and 2030. Diabetes Res. Clin. Pract. 87, 4-14 (2010).
4. McCarthy, M.I. Genomics, type 2 diabetes, and obesity. N. Engl. J. Med. 363, 2339-2350 (2010).
5. Jowett, J.B. et al. Genetic influences on type 2 diabetes and metabolic syndrome related quantitative traits in Mauritius. Twin Res. Hum. Genet. 12, 44-52 (2009).
6. Chambers, J.C. et al. Genetic variation in SCN10A influences cardiac conduction. Nat. Genet. 42, 149-152 (2010).
7. Saleheen, D. et al. The Pakistan Risk of Myocardial Infarction Study: a resource for the study of genetic, lifestyle and other determinants of myocardial infarction in South Asia. Eur. J. Epidemiol. 24, 329-338 (2009).
8. Lavanya, R. et al. Methodology of the Singapore Indian Chinese Cohort (SICC) eye study: quantifying ethnic variations in the epidemiology of eye diseases in Asians. Ophthalmic Epidemiol. 16, 325-336 (2009).
9. Price, A.L. et al. Principal components analysis corrects for stratification in genome-wide association studies. Nat. Genet. 38, 904-909 (2006). (Pubitemid 44141658)
10. Sladek, R. et al. A genome-wide association study identifies novel risk loci for type 2 diabetes. Nature 445, 881-885 (2007).
11. Voight, B.F. et al. Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis. Nat. Genet. 42, 579-589 (2010).
12. Kahn, S.E., Hull, R.L. & Utzschneider, K.M. Mechanisms linking obesity to insulin resistance and type 2 diabetes. Nature 444, 840-846 (2006). (Pubitemid 46024990)
13. -1000 Genomes Project Consortium. et al. A map of human genome variation from population-scale sequencing. Nature 467, 1061-1073 (2010).
14. Heid, I.M. et al. Meta-analysis identifies 13 new loci associated with waist-hip ratio and reveals sexual dimorphism in the genetic basis of fat distribution. Nat. Genet. 42, 949-960 (2010).
15. Chambers, J.C. et al. Common genetic variation near MC4R is associated with waist circumference and insulin resistance. Nat. Genet. 40, 716-718 (2008). (Pubitemid 351748872)
16. Kooner, J.S. et al. Genome-wide scan identifies variation in MLXIPL associated with plasma triglycerides. Nat. Genet. 40, 149-151 (2008). (Pubitemid 351171393)
17. Coronary Artery Disease (C4D) Genetics Consortium. A genome-wide association study in Europeans and South Asians identifies five new loci for coronary artery disease. Nat. Genet. 43, 339-344 (2011).
18. Dufresne, A.M. & Smith, R.J. The adapter protein GRB10 is an endogenous negative regulator of insulin-like growth factor signaling. Endocrinology 146, 4399-4409 (2005). (Pubitemid 41324037)
19. Depetris, R.S., Wu, J. & Hubbard, S.R. Structural and functional studies of the Ras-associating and pleckstrin-homology domains of Grb10 and Grb14. Nat. Struct. Mol. Biol. 16, 833-839 (2009).
20. Holt, L.J. et al. Dual ablation of Grb10 and Grb14 in mice reveals their combined role in regulation of insulin signaling and glucose homeostasis. Mol. Endocrinol. 23, 1406-1414 (2009).
21. Woodard-Grice, A.V., McBrayer, A.C., Wakefield, J.K., Zhuo, Y. & Bellis, S.L. Proteolytic shedding of ST6Gal-I by BACE1 regulates the glycosylation and function of 4-1 integrins. J. Biol. Chem. 283, 26364-26373 (2008).
22. Maeda, N. et al. Diet-induced insulin resistance in mice lacking adiponectin/ ACRP30. Nat. Med. 8, 731-737 (2002). (Pubitemid 34778727)
23. Siitonen, N. et al. Association of ADIPOQ gene variants with body weight, type 2 diabetes and serum adiponectin concentrations: the Finnish Diabetes Prevention Study. BMC Med. Genet. 12, 5 (2011).
24. Seaman, M.N., Marcusson, E.G., Cereghino, J.L. & Emr, S.D. Endosome to Golgi retrieval of the vacuolar protein sorting receptor, Vps10p, requires the function of the VPS29, VPS30, and VPS35 gene products. J. Cell Biol. 137, 79-92 (1997). (Pubitemid 27167297)
25. Seaman, M.N., Harbour, M.E., Tattersall, D., Read, E. & Bright, N. Membrane recruitment of the cargo-selective retromer subcomplex is catalysed by the small GTPase Rab7 and inhibited by the Rab-GAP TBC1D5. J. Cell Sci. 122, 2371-2382 (2009).
26. Kim, E. et al. Identification of novel retromer complexes in the mouse testis. Biochem. Biophys. Res. Commun. 375, 16-21 (2008).
27. Dell Angelica, E.C. et al. AP-3: an adaptor-like protein complex with ubiquitous expression. EMBO J. 16, 917-928 (1997).
28. Brasaemle, D.L. et al. Perilipin A increases triacylglycerol storage by decreasing the rate of triacylglycerol hydrolysis. J. Biol. Chem. 275, 38486-38493 (2000). (Pubitemid 32009175)
29. Qi, L. et al. Genetic variation at the perilipin (PLIN) locus is associated with obesity-related phenotypes in White women. Clin. Genet. 66, 299-310 (2004). (Pubitemid 39317631)
30. Beller, M. et al. PERILIPIN-dependent control of lipid droplet structure and fat storage in Drosophila. Cell Metab. 12, 521-532 (2010).
31. Sumoy, L. et al. HMG20A and HMG20B map to human chromosomes 15q24 and 19p13.3 and constitute a distinct class of HMG-box genes with ubiquitous expression. Cytogenet. Cell Genet. 88, 62-67 (2000). (Pubitemid 30175597)
32. Artegiani, B. et al. The interaction with HMG20a/b proteins suggests a potential role for ?-dystrobrevin in neuronal differentiation. J. Biol. Chem. 285, 24740-24750 (2010).
33. Battle, M.A. et al. Hepatocyte nuclear factor 4? orchestrates expression of cell adhesion proteins during the epithelial transformation of the developing liver. Proc. Natl. Acad. Sci. USA 103, 8419-8424 (2006). (Pubitemid 43838470)
34. Harries, L.W., Brown, J.E. & Gloyn, A.L. Species-specific differences in the expression of the HNF1A, HNF1B and HNF4A genes. PLoS ONE 4, e7855 (2009).
35. Yamagata, K. et al. Mutations in the hepatocyte nuclear factor-4? gene in maturity-onset diabetes of the young (MODY1). Nature 384, 458-460 (1996). (Pubitemid 26414661)
36. Teo, Y.Y. et al. Singapore Genome Variation Project: a haplotype map of three Southeast Asian populations. Genome Res. 19, 2154-2162 (2009).
37. Chidambaram, M., Radha, V. & Mohan, V. Replication of recently described type 2 diabetes gene variants in a South Indian population. Metabolism 59, 1760-1766 (2010).
38. Jafar, T.H. et al. Community-based interventions to promote blood pressure control in a developing country: a cluster randomized trial. Ann. Intern. Med. 151, 593-601 (2009).
39. Bellary, S. et al. Enhanced diabetes care to patients of South Asian ethnic origin (the United Kingdom Asian Diabetes Study): a cluster randomised controlled trial. Lancet 371, 1769-1776 (2008). (Pubitemid 351697952)
40. Rees, S.D. et al. An FTO variant is associated with type 2 diabetes in South Asian populations after accounting for body mass index and waist circumference. Diabet. Med. 28, 673-680 (2011).
41. Söderberg, S. et al. High incidence of type 2 diabetes and increasing conversion rates from impaired fasting glucose and impaired glucose tolerance to diabetes in Mauritius. J. Intern. Med. 256, 37-47 (2004). (Pubitemid 38813618)
42. Takeuchi, F. et al. Common variants at the GCK, GCKR, G6PC2-ABCB11 and MTNR1B loci are associated with fasting glucose in two Asian populations. Diabetologia 53, 299-308 (2010).
43. Sanghera, D.K. et al. The Khatri Sikh Diabetes Study (SDS): study design, methodology, sample collection, and initial results. Hum. Biol. 78, 43-63 (2006). (Pubitemid 44087146)
44. Katulanda, P. et al. Prevalence and projections of diabetes and pre-diabetes in adults in Sri Lanka-Sri Lanka Diabetes, Cardiovascular Study (SLDCS). Diabet. Med. 25, 1062-1069 (2008).
45. Marchini, J., Howie, B., Myers, S., McVean, G. & Donnelly, P. A new multipoint method for genome-wide association studies by imputation of genotypes. Nat. Genet. 39, 906-913 (2007). (Pubitemid 47014502)
46. Reich, D., Thangaraj, K., Patterson, N., Price, A.L. & Singh, L. Reconstructing Indian population history. Nature 461, 489-494 (2009).
47. Bacanu, S.A., Devlin, B. & Roeder, K. The power of genomic control. Am. J. Hum. Genet. 66, 1933-1944 (2000). (Pubitemid 30480100)
48. Li, H. & Durbin, R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26, 589-595 (2010).
49. Li, R. et al. SNP detection for massively parallel whole-genome resequencing. Genome Res. 19, 1124-1132 (2009).
50. Ong, R.T. & Teo, Y.Y. varLD: a program for quantifying variation in linkage disequilibrium patterns between populations. Bioinformatics 26, 1269-1270 (2010).
51. Myers, A.J. et al. A survey of genetic human cortical gene expression. Nat. Genet. 39, 1494-1499 (2007). (Pubitemid 350191339)
52. Webster, J.A. et al. Genetic control of human brain transcript expression in Alzheimer disease. Am. J. Hum. Genet. 84, 445-458 (2009).
53. Dixon, A.L. et al. A genome-wide association study of global gene expression. Nat. Genet. 39, 1202-1207 (2007). (Pubitemid 47482680)
54. Ge, B. et al. Global patterns of cis variation in human cells revealed by high-density allelic expression analysis. Nat. Genet. 41, 1216-1222 (2009).
55. Dimas, A.S. et al. Common regulatory variation impacts gene expression in a cell type-dependent manner. Science 325, 1246-1250 (2009).
56. Schadt, E.E. et al. Mapping the genetic architecture of gene expression in human liver. PLoS Biol. 6, e107 (2008).
57. Nica, A.C. et al. The architecture of gene regulatory variation across multiple human tissues: the MuTHER study. PLoS Genet. 7, e1002003 (2011).