A genome-wide association study identifies 2 susceptibility loci for crohn's disease in a Japanese population

Gastroenterology

Volumn 144, Issue 4, 2013, Pages 781-788

  Yamazaki, Keiko ^a   Umeno, Junji ^a,b   Takahashi, Atsushi ^a   Hirano, Atsushi ^a,b   Johnson, Todd Andrew ^a   Kumasaka, Natsuhiko ^a   Morizono, Takashi ^a   Hosono, Naoya ^a   Kawaguchi, Takaaki ^c   Takazoe, Masakazu ^c   Yamada, Tetsuhiro ^d   Suzuki, Yasuo ^d   Tanaka, Hiroki ^e   Motoya, Satoshi ^e,f   Hosokawa, Masayo ^f   Arimura, Yoshiaki ^f   Shinomura, Yasuhisa ^f   Matsui, Toshiyuki ^g   Matsumoto, Takayuki ^b   Iida, Mitsuo ^b   Tsunoda, Tatsuhiko ^a   Nakamura, Yusuke ^h   Kamatani, Naoyuki ^a   Kubo, Michiaki ^a   more..

^a INST OF PHYS AND CHEMICAL RESEARCH   (Japan)

^b KYUSHU UNIVERSITY   (Japan)

^c Social Insurance Chuo General Hospital   (Japan)

^d TOHO UNIVERSITY   (Japan)

^e Sapporo Kosei General Hospital   (Japan)

^f SAPPORO MEDICAL UNIVERSITY SCHOOL OF MEDICINE   (Japan)

^g Fukuoka University Chikushi Hospital   (Japan)

^h UNIVERSITY OF TOKYO   (Japan)

Author keywords

CD; GWAS; Inflammatory Bowel Disease; Polymorphism

Indexed keywords

ADULT; ARTICLE; CHROMOSOME 4P; COHORT ANALYSIS; CONTROLLED STUDY; CROHN DISEASE; FEMALE; GENE LOCUS; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC SUSCEPTIBILITY; HUMAN; JAPANESE; MAJOR CLINICAL STUDY; MAJOR HISTOCOMPATIBILITY COMPLEX; MALE; PRIORITY JOURNAL; REPLICATION STUDY;

EID: 84875234775     PISSN: 00165085     EISSN: 15280012     Source Type: Journal    
DOI: 10.1053/j.gastro.2012.12.021     Document Type: Article

References (51)

1. D.K. Podolsky Inflammatory bowel disease N Engl J Med 347 2002 417 429
2. K. Asakura, Y. Nishiwaki, N. Inoue Prevalence of ulcerative colitis and Crohn's disease in Japan J Gastroenterol 44 2009 659 665
3. K. Goh, S. Xiao Inflammatory bowel disease: a survey of the epidemiology in Asia J Dig Dis 10 2009 1 6
4. J.H. Cho The genetics and immunopathogenesis of inflammatory bowel disease Nat Rev Immunol 8 2008 458 466
5. M.L. Budarf, C. Labbé, G. David GWA studies: rewriting the story of IBD Trends Genet 25 2009 137 146
6. K. Yamazaki, D. McGovern, J. Ragoussis Single nucleotide polymorphisms in TNFSF15 confer susceptibility to Crohn's disease Hum Mol Genet 14 2005 3499 3506
7. R.H. Duerr, K.D. Taylor, S.R. Brant A genome-wide association study identifies IL23R as an inflammatory bowel disease gene Science 314 2006 1461 1463
8. J.D. Rioux, R.J. Xavier, K.D. Taylor Genome-wide association study identifies new susceptibility loci for Crohn disease and implicates autophagy in disease pathogenesis Nat Genet 39 2007 596 604
9. J. Hampe, A. Franke, P. Rosenstiel A genome-wide association scan of nonsynonymous SNPs identifies a susceptibility variant for Crohn disease in ATG16L1 Nat Genet 39 2007 207 211
10. C. Libioulle, E. Louis, S. Hansoul Novel Crohn disease locus identified by genome-wide association maps to a gene desert on 5p13.1 and modulates expression of PTGER4 PLoS Genet 3 2007 e58
11. M. Parkes, J.C. Barrett, N.J. Prescott Sequence variants in the autophagy gene IRGM and multiple other replicating loci contribute to Crohn's disease susceptibility Nat Genet 39 2007 830 832
12. The Wellcome Trust Case Control Consortium Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls Nature 447 2007 661 678
13. J.C. Barrett, S. Hansoul, D.L. Nicolae Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease Nat Genet 40 2008 955 962
14. A. Franke, D.P.B. McGovern, J.C. Barrett Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci Nat Genet 42 2010 1118 1125
15. T.A. Manolio, F.S. Collins, N.J. Cox Finding the missing heritability of complex diseases Nature 461 2009 747 753
16. I. Hilmi, Y.M. Tan, K.L. Goh Crohn's disease in adults: observations in a multiracial Asian population World J Gastroenterol 12 2006 1435 1438
17. Y.F. Wang, H. Zhang, Q. Ouyang Clinical manifestations of inflammatory bowel disease: East and West differences J Dig Dis 8 2007 121 127
18. K. Yamazaki, M. Takazoe, T. Tanaka Absence of mutation in the NOD2/CARD15 gene among 483 Japanese patients with Crohn's disease J Hum Genet 47 2002 469 472
19. K. Yamazaki, Y. Onouchi, M. Takazoe Association analysis of genetic variants in IL23R, ATG16L1 and 5p13.1 loci with Crohn's disease in Japanese patients J Hum Genet 52 2007 575 583
20. K. Yamazaki, A. Takahashi, M. Takazoe Positive association of genetic variants in the upstream region of NKX2-3 with Crohn's disease in Japanese patients Gut 58 2009 228 232
21. Y. Okada, K. Yamazaki, J. Umeno HLA-Cw*1202-B*5201- DRB1*1502 haplotype increases risk for ulcerative colitis but reduces risk for Crohn's disease Gastroenterology 141 2011 864 871.e1-5
22. J.E. Lennard-Jones Classification of inflammatory bowel disease Scand J Gastroenterol Suppl 170 1989 2 6 discussion, 16-9
23. K. Asano, T. Matsushita, J. Umeno A genome-wide association study identifies three new susceptibility loci for ulcerative colitis in the Japanese population Nat Genet 41 2009 1325 1329
24. Y. Nakamura The BioBank Japan Project Clin Adv Hematol Oncol 5 2007 696 697
25. The International Hapmap Consortium A haplotype map of the human genome Nature 437 2005 1299 1320
26. Y. Yamaguchi-Kabata, K. Nakazono, A. Takahashi Japanese population structure, based on SNP genotypes from 7003 individuals compared to other ethnic groups: effects on population-based association studies Am J Hum Genet 83 2008 445 456
27. Y. Okada, T. Hirota, Y. Kamatani Identification of nine novel loci associated with white blood cell subtypes in a Japanese population PLoS Genetics 7 2011 e1002067
28. B.N. Howie, P. Donnelly, J. Marchini A flexible and accurate genotype imputation method for the next generation of genome-wide association studies PLoS Genet 5 2009 e1000529
29. The 1000 Genomes Project Consortium A map of human genome variation from population-scale sequencing Nature 467 2010 1061 1073
30. J. Zheng, Y. Li, G.R. Abecasis A comparison of approaches to account for uncertainty in analysis of imputed genotypes Genet Epidemiol 35 2011 102 110
31. Y. Li, C.J. Willer, J. Ding MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes Genet Epidemiol 34 2010 816 834
32. J. Barrett, B. Fry, J. Maller Haploview: analysis and visualization of LD and haplotype maps Bioinformatics 21 2005 263 265
33. Hirano A, Yamazaki K, Umeno J, et al. Association study of 71 European Crohn's disease susceptibility loci in a Japanese population. Inflamm Bowel Dis. In press.
34. S. Raychaudhuri, R.M. Plenge, E.J. Rossin Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions PLoS Genet 5 2009 e1000534
35. E.J. Rossin, K. Lage, S. Raychaudhuri Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology PLoS Genet 7 2011 e1001273
36. P.I.W. de Bakker, M.A.R. Ferreira, X. Jia Practical aspects of imputation-driven meta-analysis of genome-wide association studies Hum Mol Genet 17 2008 R122 R1228
37. A.L. Price, N.J. Patterson, R.M. Plenge Principal components analysis corrects for stratification in genome-wide association studies Nat Genet 38 2006 904 909
38. S.B. Gabriel, S.F. Schaffner, H. Nguyen The structure of haplotype blocks in the human genome Science 296 2002 2225 2229
39. S. Purcell, B. Neale, K. Todd-Brown PLINK: a tool set for whole-genome association and population-based linkage analyses Am J Hum Genet 81 2007 559 575
40. B.E. Stranger, M.S. Forrest, M. Dunning Relative impact of nucleotide and copy number variation on gene expression phenotypes Science 315 2007 848 853
41. P. Danecek, A. Auton, G. Abecasis The variant call format and VCFtools Bioinformatics 27 2011 2156 2158
42. J. Yang, W. Yang, N. Hirankarn ELF1 is associated with systemic lupus erythematosus in Asian populations Hum Mol Genet 20 2011 601 607
43. Y. Okada, K. Shimane, Y. Kochi A genome-wide association study identified AFF1 as a susceptibility locus for systemic lupus eyrthematosus in Japanese PLoS Genet 8 2012 e1002455
44. L. Jostins, S. Ripke, R.K. Weersma Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease Nature 490 2012 119 124
45. T. Kawai, S. Akira The role of pattern-recognition receptors in innate immunity: update on Toll-like receptors Nat Immunol 11 2010 373 384
46. S. Sarafova, G. Siu A potential role for Elf-1 in CD4 promoter function J Biol Chem 274 1999 16126 16134
47. H.-J. Choi, Y. Geng, H. Cho Differential requirements for the Ets transcription factor Elf-1 in the development of NKT cells and NK cells Blood 117 2011 1880 1887
48. L.T. Mars, L. Araujo, P. Kerschen Invariant NKT cells inhibit development of the Th17 lineage Proc Natl Acad Sci U S A 106 2009 6238 6243
49. J.A. Camacho, C. Obie, B. Biery Hyperornithinaemia-hyperammonaemia- homocitrullinuria syndrome is caused by mutations in a gene encoding a mitochondrial ornithine transporter Nat Genet 22 1999 151 158
50. M.T. Bedford, R. Reed, P. Leder WW domain-mediated interactions reveal a spliceosome-associated protein that binds a third class of proline-rich motif: the proline glycine and methionine-rich motif Proc Natl Acad Sci U S A 95 1998 10602 10607
51. M.C. Vegliante, C. Royo, J. Palomero Epigenetic activation of SOX11 in lymphoid neoplasms by histone modifications PLoS One 6 2011 e21382