An investigation of genome-wide studies reported susceptibility loci for ulcerative colitis shows limited replication in North Indians

PLoS ONE

Volumn 6, Issue 1, 2011, Pages

  Juyal, Garima ^a   Prasad, Pushplata ^a   Senapati, Sabyasachi ^a   Midha, Vandana ^b   Sood, Ajit ^b   Amre, Devendra ^c,d   Juyal, Ramesh C ^e   Thelma, B K ^a  

^a UNIVERSITY OF DELHI   (India)

^b DAYANAND MEDICAL COLLEGE AND HOSPITAL   (India)

^c UNIVERSITÉ DE MONTRÉAL   (Canada)

^d UNIVERSITY OF MONTREAL   (Canada)

^e NATIONAL INSTITUTE OF IMMUNOLOGY   (India)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CAUCASIAN; COHORT ANALYSIS; CONTROLLED STUDY; CROHN DISEASE; ETHNIC DIFFERENCE; GENE FREQUENCY; GENE IDENTIFICATION; GENE LOCUS; GENE REPLICATION; GENETIC ASSOCIATION; GENETIC RISK; GENETIC SUSCEPTIBILITY; GENOTYPE; HAPLOTYPE MAP; HUMAN; INDIAN; MAJOR CLINICAL STUDY; PHENOTYPE; POPULATION GENETICS; SINGLE NUCLEOTIDE POLYMORPHISM; ULCERATIVE COLITIS; CASE CONTROL STUDY; ETHNIC GROUP; ETHNOLOGY; GENETIC PREDISPOSITION; GENETICS; INDIA;

CASE-CONTROL STUDIES; COLITIS, ULCERATIVE; CROHN DISEASE; ETHNIC GROUPS; GENETIC LOCI; GENETIC PREDISPOSITION TO DISEASE; GENOME-WIDE ASSOCIATION STUDY; HUMANS; INDIA; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 79551652513     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0016565     Document Type: Article

References (33)

1. Sood A, Midha V, Sood N, Bhatia AS, Avasthi G (2003) Incidence and prevalence of ulcerative colitis in Punjab, North India. Gut 52(11): 1587-90.
2. Fisher SA, Tremelling M, Anderson CA, Gwilliam R, Bumpstead S, et al. (2008) Genetic determinants of ulcerative colitis include the ECM1 locus and five loci implicated in Crohn's disease. Nat Genet 40(6): 710-712.
3. Franke A, Balschun T, Karlsen TH, Sventoraityte J, Nikolaus S, et al. (2008) Sequence variants in IL10, ARPC2 and multiple other loci contribute to ulcerative colitis susceptibility. Nat Genet 40(11): 1319-23.
4. Silverberg MS, Cho JH, Rioux JD, McGovern DP, Wu J, Annese V, et al. (2009) Ulcerative colitis-risk loci on chromosomes 1p36 and 12q15 found by genomewide association study. Nat Genet 2009; 41(2): 216-20.
5. Franke A, Balschun T, Sina C, Ellinghaus D, Häsler R, et al. (2010) Genomewide association study for ulcerative colitis identifies risk loci at 7q22and 22q13 (IL17REL). Nat Genet 2010; 42(4): 292-4.
6. McGovern DP, Gardet A, Törkvist L, Goyette P, Essers J, et al. (2010) Genomewide association identifies multiple ulcerative colitis susceptibility loci. Nat Genet 42(4): 332-7.
7. Asano K, Matsuhita T, Umeno J, Hosono N, Takahashi A, et al. (2009) A genome-wide association study identifies three new susceptibility loci for ulcerative colitis in the Japanese population. Nature Genetics 41: 1325-1329.
8. Yamazaki K, McGovern D, Ragoussis J, Paolucci M, Butler H, et al. (2005) Single nucleotide polymorphisms in TNFSF15 confer susceptibility to Crohn's disease. Hum Mol Genet 15; 14(22): 3499-506.
9. Duerr RH, Taylor KD, Brant SR, Rioux JD, Silverberg MS, et al. (2006) A genome-wide association study identifies IL23R as an inflammatory bowel disease gene. Science 314(5804): 1461-3.
10. Hampe J, Franke A, Rosenstiel P, Till A, Teuber M, et al. (2007) A genome-wide association scan of nonsynonymous SNPs identifies a susceptibility variant for Crohn disease in ATG16L1. Nat Genet 39(2): 207-11.
11. Barrett JC, Hansoul S, Nicolae DL, Cho JH, Duerr RH, et al. (2008) Genomewide association defines more than 30 distinct susceptibility loci for Crohn's disease. Nat Genet 40(8): 955-62.
12. The Wellcome Trust Case Control Consortium (2007) Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 447: 661-678.
13. Franke A, Balschun T, Karlsen TH, Hedderich J, May S, et al. (2008) Replication of signals from recent studies of Crohn's disease identifies previously unknown disease loci for ulcerative colitis. Nat Genet 40(6): 713-5.
14. Zhernakova A, van Diemen CC, Wijmenga C (2009) Detecting shared pathogenesis from the shared genetics of immune-related diseases. Nat Rev Genet 10(1): 43-55.
15. Budarf ML, Labbe C, David G, Rioux JD (2009) GWA studies: rewriting the story of IBD. Trends Genet 25: 137-46.
16. Juyal G, Amre D, Midha V, Sood A, Seidman E, et al. (2007) Evidence of allelic heterogeneity for associations between the NOD2/CARD15 gene and ulcerative colitis among North Indians. Aliment Pharmacol Ther 26(10): 1325-32.
17. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, et al. (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81(3): 559-75.
18. Weersma RK, Zhernakova A, Nolte IM, Lefebvre C, Rioux JD, et al. (2008) ATG16L1 and IL23R are associated with inflammatory bowel diseases but not with celiac disease in the Netherlands. Am J Gastroenterol 103(3): 621-7.
19. Tremelling M, Cummings F, Fisher SA, Mansfield J, Gwilliam R, et al. (2007) IL23R variation determines susceptibility but not disease phenotype in inflammatory bowel disease. Gastroenterology 132(5): 1657-64.
20. UK IBD Genetics Consortium, Barrett JC, Lee JC, Lees CW, Prescott NJ, et al. (2009) Genome-wide association study of ulcerative colitis identifies three new susceptibility loci, including the HNF4A region. Nat Genet 41(12): 1330-4.
21. Raelson JV, Little RD, Ruether A, Fournier H, Paquin B, et al. (2007) Genomewide association study for Crohn's disease in the Quebec Founder Population identifies multiple validated disease loci. Proc Natl Acad Sci 104(37): 14747-52.
22. Roberts RL, Gearry RB, Hollis-Moffatt JE, Miller AL, Reid J, et al. (2007) IL23R R381Q and ATG16L1 T300A are strongly associated with Crohn's disease in a study of New Zealand Caucasians with inflammatory bowel disease. Am J Gastroenterol 102(12): 2754-61.
23. Büning C, Schmidt HH, Molnar T, De Jong DJ, Fiedler T, et al. (2007) Heterozygosity for IL23R p.Arg381Gln confers a protective effect not only against Crohn's disease but also ulcerative colitis. Aliment Pharmacol Ther 26(7): 1025-33.
24. Yang SK, Park M, Lim J, Park SH, Ye BD, et al. (2009) Contribution of IL23R but not ATG16L1 to Crohn's disease susceptibility in Koreans. Inflamm Bowel Dis 15(9): 1385-90.
25. Yamazaki K, Onouchi Y, Takazoe M, Kubo M, Nakamura Y, et al. (2007) Association analysis of genetic variants in IL23R, ATG16L1 and 5p13.1 loci with Crohn's disease in Japanese patients. J Hum Genet 52(7): 575-83.
26. Bin C, Zhirong Z, Xiaoqin W, Minhu C, Mei L, et al. (2009) Contribution of rs11465788 in IL23R gene to Crohn's disease susceptibility and phenotype in Chinese population. J Genet 88(2): 191-6.
27. Madsen KL, Doyle JS, Tavernini MM, Jewell LD, Rennie RP, et al. (2000) Antibiotic therapy attenuates colitis in interleukin 10 gene-deficient mice. Gastroenterology 118: 1094-1105.
28. Rajkumar R, Kashyap VK (2004) Genetic structure of four socio-culturally diversified caste populations of southwest India and their affinity with related Indian and global groups. BMC Genetics 5: 23.
29. Mochida A, Kinouchi Y, Negoro K, Takahashi S, Takagi S, et al. (2007) Butyrophilin-like 2 gene is associated with ulcerative colitis in the Japanese under strong linkage disequilibrium with HLA-DRB1*1502. Tissue Antigens 70: 128-35.
30. Fisher SA, Tremelling M, Anderson CA, Gwilliam R, Bumpstead S, et al. (2008) Genetic determinants of ulcerative colitis include the ECM1 locus and five loci implicated in Crohn's disease. Nat Genet 40: 710-2.
31. Hugot JP, Zaccaria I, Cavanaugh J, Yang H, Vermeire S, et al. (2007) Prevalence of CARD15 /NOD2 mutations in Caucasian healthy people. Am J Gastroenterol 102: 1259-67.
32. Mathew CG, Lewis CM (2004) Genetics of inflammatory bowel disease: progress and prospects. Hum Mol Genet 13: 161-8.
33. Kakuta Y, Kinouchi Y, Negoro K, Takahashi S, Shimosegawa T (2006) Association study of TNFSF15 polymorphisms in Japanese patients with inflammatory bowel disease. Gut 55(10): 1527-8).