Genome-wide association scan in north Indians reveals three novel HLA-independent risk loci for ulcerative colitis

Gut

Volumn 64, Issue 4, 2015, Pages 571-579

  Juyal, Garima ^a   Negi, Sapna ^a   Sood, Ajit ^b,c   Gupta, Aditi ^a   Prasad, Pushplata ^a   Senapati, Sabyasachi ^a   Zaneveld, Jacques ^d   Singh, Shalini ^a   Midha, Vandana ^c   Van Sommeren, Suzanne ^e   Weersma, Rinse K ^e   Ott, Jurg ^f   Jain, Sanjay ^a   Juyal, Ramesh C ^a   Thelma, B K ^a  

^a UNIVERSITY OF DELHI   (India)

^b NATIONAL INSTITUTE OF IMMUNOLOGY   (India)

^c DAYANAND MEDICAL COLLEGE AND HOSPITAL   (India)

^d BAYLOR COLLEGE OF MEDICINE   (United States)

^e UNIVERSITY MEDICAL CENTER GRONINGEN   (Netherlands)

^f INSTITUTE OF PSYCHOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ALTERNATIVE COMPLEMENT PATHWAY C3 C5 CONVERTASE; HLA ANTIGEN;

ARTICLE; BAT2 GENE; CASE CONTROL STUDY; CFB GENE; CHROMOSOME 6; CONTROLLED STUDY; GENE; GENE LOCUS; GENETIC ASSOCIATION; GENETIC HETEROGENEITY; GENOTYPE; HSPA1L GENE; HUMAN; INDIAN; MAJOR CLINICAL STUDY; MSH5 GENE; NOTCH4 GENE; PRIORITY JOURNAL; QUALITY CONTROL; SINGLE NUCLEOTIDE POLYMORPHISM; SLC44A4 GENE; ULCERATIVE COLITIS; CAUCASIAN; GENETICS; RISK;

CASE-CONTROL STUDIES; COLITIS, ULCERATIVE; EUROPEAN CONTINENTAL ANCESTRY GROUP; GENOME-WIDE ASSOCIATION STUDY; HLA ANTIGENS; HUMANS; POLYMORPHISM, SINGLE NUCLEOTIDE; RISK;

EID: 84924414804     PISSN: 00175749     EISSN: 14683288     Source Type: Journal    
DOI: 10.1136/gutjnl-2013-306625     Document Type: Article

References (36)

1. Molodecky NA, Soon IS, Rabi DM, et al. Increasing incidence and prevalence of the inflammatory bowel diseases with time, based on systematic review. Gastroenterology 2012;142:46-54.
2. Zhang H, Massey D, Tremelling M, et al. Genetics of inflammatory bowel disease: clues to pathogenesis. Br Med Bull 2008;87:17-30.
3. Cho JH, Brant SR. Recent insights into the genetics of inflammatory bowel disease. Gastroenterology 2011;140:1704-12.
4. Barrett JC, Lee JC, Lees CW, et al.; UK IBD Genetics Consortium. Genome-wide association study of ulcerative colitis identifies three new susceptibility loci, including the HNF4A region. Nat Genet 2009;41:1330-4.
5. McGovern DP, Gardet A, Törkvist L, et al. Genome-wide association identifies multiple ulcerative colitis susceptibility loci. Nat Genet 2010;42:332-7.
6. Anderson CA, Boucher G, Lees CW, et al. Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47. Nat Genet 2011;43:246-52.
7. Jostins L, Ripke S, Weersma RK, et al. Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. Nature 2012;491: 119-24.
8. McCarthy MI. Casting a wider net for diabetes susceptibility genes. Nat Genet 2008;40:1039-40.
9. Waters KM, Le Marchand L, Kolonel LN, et al. Generalizability of associations from prostate cancer genome-wide association studies in multiple populations. Cancer Epidemiol Biomarkers Prev 2009;18:1285-9.
10. Yamada H, Penney KL, Takahashi H, et al. Replication of prostate cancer risk loci in a Japanese case-control association study. J Natl Cancer Inst 2009;101: 1330-6.
11. Asano K, Matsushita T, Umeno J, et al. A genome-wide association study identifies three new susceptibility loci for ulcerative colitis in the Japanese population. Nat Genet 2009;41:1325-9.
12. Yamazaki K, Takazoe M, Tanaka T, et al. Absence of mutation in the NOD2/ CARD15 gene among 483 Japanese patients with Crohn's disease. J Hum Genet 2002;47:469-72.
13. Yamazaki K, Onouchi Y, Takazoe M, et al. Association analysis of genetic variants in IL23R, ATG16L1 and 5p13.1 loci with Crohn's disease in Japanese patients. J Hum Genet 2007;52:575-83.
14. Juyal G, Amre D, Midha V, et al. Evidence of allelic heterogeneity for associations between the NOD2/CARD15 gene and ulcerative colitis among North Indians. Aliment Pharmacol Ther 2007;26:1325-32.
15. Juyal G, Midha V, Amre D, et al. Associations between common variants in the MDR1 gene and ulcerative colitis among North Indians. Pharmacogenet Genomics 2009;19:77-85.
16. Juyal G, Prasad P, Senapati S, et al. An investigation of genome-wide studies reported susceptibility loci for ulcerative colitis shows limited replication in north Indians. PLOS One 2011;6:e16565.
17. Yang SK, Hong M, Zhao W, et al. Genome-wide association study of ulcerative colitis in Koreans suggests extensive overlapping of genetic susceptibility with Caucasians. Inflamm Bowel Dis 2013;19:954-66.
18. Purcell S, Neale B, Todd-Brown K, et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 2007;81:559-75.
19. Price AL, Patterson NJ, Plenge RM, et al. Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 2006;38: 904-9.
20. Sawcer S, Hellenthal G, Pirinen M, et al.; International Multiple Sclerosis Genetics Consortium, Wellcome Trust Case Control Consortium. Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis. Nature 2011;476:214-19.
21. Korte A, Vilhjálmsson BJ, Segura V, et al. A mixed-model approach for genome-wide association studies of correlated traits in structured populations. Nat Genet 2012;44:1066-71.
22. Tsoi LC, Spain SL, Knight J, et al. Identification of 15 new psoriasis susceptibility loci highlights the role of innate immunity. Nat Genet 2012;44:1341-8.
23. Raychaudhuri S, Plenge RM, Rossin EJ, et al. Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions. PLOS Genet 2009;5:e1000534.
24. Stranger BE, Montgomery SB, Dimas AS, et al. Patterns of cis regulatory variation in diverse human populations. PLOS Genet 2012;8:e1002639.
25. Pirinen M, Donnelly P, Spencer CC. Including known covariates can reduce power to detect genetic effects in case-control studies. Nat Genet 2012;44: 848-51.
26. Liu JZ, Hov JR, Folseraas T, et al. Dense genotyping of immune-related disease regions identifies nine new risk loci for primary sclerosing cholangitis. Nature Genet 2013;45:670-5.
27. Negi S, Juyal G, Senapati S, et al. A genome-wide association study reveals ARL15, a novel non-HLA susceptibility gene for Rheumatoid arthritis in north Indians. Arthritis Rheum 2013;65:3026-35.
28. Cipriani V, Leung HT, Plagnol V, et al. Genome-wide association study of age-related macular degeneration identifies associated variants in the TNXB-FKBPL-NOTCH4 region of chromosome 6p21.3. Hum Mol Genet 2012;21:4138-50.
29. van Heel DA, Udalova IA, De Silva AP, et al. Inflammatory bowel disease is associated with a TNF polymorphism that affects an interaction between the OCT1 and NF-κB transcription factor. Hum Mol Genet 2002;11:1281-89.
30. Okamoto K, Makino S, Yoshikawa Y, et al. Identification of IκBL as the second major histocompatibility complex-linked susceptibility locus for rheumatoid arthritis. Am J Hum Genet 2003;72:303-12.
31. Rioux JD, Goyette P, Vyse TJ, et al.; International MHC and Autoimmunity Genetics Network. Mapping of multiple susceptibility variants within the MHC region for 7 immune-mediated diseases. Proc Natl Acad Sci 2009;106:18680-5.
32. Khor CC, Chau TN, Pang J, et al. Genome-wide association study identifies susceptibility loci for dengue shock syndrome at MICB and PLCE1. Nat Genet 2011;43:1139-41.
33. Fernando MM, Freudenberg J, Lee A, et al. Transancestral mapping of the MHC region in systemic lupus erythematosus identifies new independent and interacting loci at MSH5, HLA-DPB1 and HLA-G. Ann Rheum Dis 2012;71:777-84.
34. Solovieff N, Cotsapas C, Lee PH, et al. Pleiotropy in complex traits: challenges and strategies. Nat Rev Genet 2013;14:483-95.
35. Tjonneland A, Overvad K, Bergmann MM, et al.; IBD in EPIC Study Investigators. Linoleic acid, a dietary n-6 polyunsaturated fatty acid, and the aetiology of ulcerative colitis: a nested case-control study within a European prospective cohort study. Gut 2009;58:1606-11.
36. Mahid SS, Minor KS, Soto RE, et al. Smoking and inflammatory bowel disease: a meta-analysis. Mayo Clin Proc 2006;81:1462-71.