Single-nucleotide polymorphisms in inflammatory bowel disease

Translational Research

Volumn 160, Issue 1, 2012, Pages 45-64

  Neuman, Manuela G ^a   Nanau, Radu M ^a  

^a UNIVERSITY OF TORONTO   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

BETA CATENIN; CASPASE; CASPASE RECRUITMENT DOMAIN PROTEIN 15; CASPASE RECRUITMENT DOMAIN PROTEIN 4; CHEMOKINE RECEPTOR CXCR3; GAMMA INTERFERON; HLA ANTIGEN; HLA ANTIGEN CLASS 2; IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; INTERLEUKIN 10; INTERLEUKIN 12; INTERLEUKIN 22; INTERLEUKIN 23; INTERLEUKIN 23 RECEPTOR; INTERLEUKIN 26; JANUS KINASE 2; MACROPHAGE ACTIVATING FACTOR; MAJOR HISTOCOMPATIBILITY ANTIGEN CLASS 3; MYOSIN; MYOSIN 9B PROTEIN; ORGANIC CATION TRANSPORTER; SLC22A4 PROTEIN; STAT3 PROTEIN; STAT4 PROTEIN; TRANSCRIPTION FACTOR NKX2.2; TRANSCRIPTION FACTOR RUNX3; TUMOR NECROSIS FACTOR ALPHA; TUMOR NECROSIS FACTOR RECEPTOR; UNCLASSIFIED DRUG; UNINDEXED DRUG; UVOMORULIN;

ALLELE; CHROMOSOME 6P; CROHN DISEASE; DISEASE CONTROL; ENTERITIS; ENVIRONMENTAL FACTOR; GENE; GENETIC ASSOCIATION; HAPLOTYPE; HOMEOSTASIS; HUMAN; IMMUNE RESPONSE; MAJOR HISTOCOMPATIBILITY COMPLEX; MOLECULAR INTERACTION; PATHOGENESIS; PRIORITY JOURNAL; REVIEW; RISK FACTOR; SINGLE NUCLEOTIDE POLYMORPHISM; ULCERATIVE COLITIS;

EID: 83455180734     PISSN: 19315244     EISSN: 18781810     Source Type: Journal    
DOI: 10.1016/j.trsl.2011.10.006     Document Type: Review

References (79)

1. L.R. Ferguson, A.N. Shelling, B.L. Browning, C. Huebner, and I. Petermann Genes, diet and inflammatory bowel disease Mutat Res 622 2007 70 83
2. F. Carbonnel, P. Jantchou, E. Monnet, and J. Cosnes Environmental risk factors in Crohn's disease and ulcerative colitis: an update Gastroenterol Clin Biol 33 2009 S145 S157
3. D.Y. Han, A.G. Fraser, P. Dryland, and L.R. Ferguson Environmental factors in the development of chronic inflammation: a case-control study on risk factors for Crohn's disease within New Zealand Mutat Res 690 2010 116 122
4. F.M. Ruemmele, M.G. El Khoury, and C. Talbotec Characteristics of inflammatory bowel disease with onset during the first year of life J Pediatr Gastroenterol Nutr 43 2006 603 609
5. S.L. Guthery, G. Mineau, R. Pimentel, M.S. Williams, and R.A. Kerber Inflammatory bowel disease aggregation in Utah kindreds Inflamm Bowel Dis 17 2011 823 830
6. R.K. Weersma, P.C. Stokkers, and I. Cleynen Confirmation of multiple Crohn's disease susceptibility loci in a large Dutch-Belgian cohort Am J Gastroenterol 104 2009 630 638
7. E.A. Trachtenberg, H. Yang, and E. Hayes HLA class II haplotype associations with inflammatory bowel disease in Jewish (Ashkenazi) and non-Jewish caucasian populations Hum Immunol 61 2000 326 333
8. J.K. Yamamoto-Furusho, L.F. Uscanga, and G. Vargas-Alarcón Polymorphisms in the promoter region of tumor necrosis factor alpha (TNF-alpha) and the HLA-DRB1 locus in Mexican mestizo patients with ulcerative colitis Immunol Lett 95 2004 31 35
9. 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
10. E.A. Festen, P.C. Stokkers, and C.C. van Diemen Genetic analysis in a Dutch study sample identifies more ulcerative colitis susceptibility loci and shows their additive role in disease risk Am J Gastroenterol 105 2010 395 402
11. G. Juyal, P. Prasad, and S. Senapati An investigation of genome-wide studies reported susceptibility loci for ulcerative colitis shows limited replication in north Indians PLoS One 6 2011 e16565
12. A. Latiano, O. Palmieri, and T. Latiano Investigation of multiple susceptibility Loci for inflammatory bowel disease in an Italian cohort of patients PLoS One 6 2011 e22688
13. R. López-Hernández, M. Valdés, and D. Lucas Association analysis of MICA gene polymorphism and MICA-129 dimorphism with inflammatory bowel disease susceptibility in a Spanish population Hum Immunol 71 2010 512 514
14. R.K. Weersma, L. Zhou, and I.M. Nolte Runt-related transcription factor 3 is associated with ulcerative colitis and shows epistasis with solute carrier family 22, members 4 and 5 Inflamm Bowel Dis 14 2008 1615 1622
15. W. Yu, Z. Lin, and A.A. Kelly Association of a Nkx2-3 polymorphism with Crohn's disease and expression of Nkx2-3 is up-regulated in B cell lines and intestinal tissues with Crohn's disease J Crohns Colitis 3 2009 189 195
16. T. Arai, Y. Kakuta, and Y. Kinouchi Increased expression of NKX2.3 mRNA transcribed from the risk haplotype for ulcerative colitis in the involved colonic mucosa Hum Immunol 72 2011 587 591
17. K. Yamazaki, A. Takahashi, and 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
18. M. Parkes, J.C. Barrett, and 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
19. N. Meggyesi, L.S. Kiss, and M. Koszarska NKX2-3 and IRGM variants are associated with disease susceptibility to IBD in Eastern European patients World J Gastroenterol 16 2010 5233 5240
20. G. John, J.P. Hegarty, and W. Yu NKX2-3 variant rs11190140 is associated with IBD and alters binding of NFAT Mol Genet Metab 104 2011 174 179
21. A. Franke, T. Balschun, and T.H. Karlsen Replication of signals from recent studies of Crohn's disease identifies previously unknown disease loci for ulcerative colitis Nat Genet 40 2008 713 715
22. L.R. Ferguson, C. Huebner, and I. Petermann Single nucleotide polymorphism in the tumor necrosis factor-alpha gene affects inflammatory bowel diseases risk World J Gastroenterol 14 2008 4652 4661
23. L.R. Ferguson, D.Y. Han, and C. Huebner Tumor necrosis factor receptor superfamily, member 1B haplotypes increase or decrease the risk of inflammatory bowel diseases in a New Zealand caucasian population Gastroenterol Res Pract 2009 2009 591704
24. J. Van Limbergen, R.K. Russell, and E.R. Nimmo IL23R Arg381Gln is associated with childhood onset inflammatory bowel disease in Scotland Gut 56 2007 1173 1174
25. M. Lacher, S. Schroepf, and J. Helmbrecht Association of the interleukin-23 receptor gene variant rs11209026 with Crohn's disease in German children Acta Paediatr 99 2010 727 733
26. L.R. Ferguson, D.Y. Han, and A.G. Fraser IL23R and IL12B SNPs and haplotypes strongly associate with Crohn's disease risk in a New Zealand population Gastroenterol Res Pract 2010 2010 539461
27. R.H. Duerr, K.D. Taylor, and S.R. Brant A genome-wide association study identifies IL23R as an inflammatory bowel disease gene Science 314 2006 1461 1463
28. C. Libioulle, E. Louis, and 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
29. L.R. Ferguson, D.Y. Han, and A.G. Fraser Genetic factors in chronic inflammation: single nucleotide polymorphisms in the STAT-JAK pathway, susceptibility to DNA damage and Crohn's disease in a New Zealand population Mutat Res 690 2010 108 115
30. K. Sato, M. Shiota, and S. Fukuda Strong evidence of a combination polymorphism of the tyrosine kinase 2 gene and the signal transducer and activator of transcription 3 gene as a DNA-based biomarker for susceptibility to Crohn's disease in the Japanese population J Clin Immunol 29 2009 815 825
31. J. Glas, J. Seiderer, and M. Nagy Evidence for STAT4 as a common autoimmune gene: rs7574865 is associated with colonic Crohn's disease and early disease onset PLoS One 5 2010 e10373
32. L.M. Diaz-Gallo, R.J. Palomino-Morales, and M. Gómez-García STAT4 gene influences genetic predisposition to ulcerative colitis but not Crohn's disease in the Spanish population: a replication study Hum Immunol 71 2010 515 519
33. C.M. Moon, J.H. Cheon, and S.W. Kim Association of signal transducer and activator of transcription 4 genetic variants with extra-intestinal manifestations in inflammatory bowel disease Life Sci 86 2010 661 667
34. J.P. Hugot, M. Chamaillard, and H. Zouali Association of NOD2 leucine-rich repeat variants with susceptibility to Crohn's disease Nature 411 2001 599 603
35. R.B. Gearry, R.L. Roberts, and M.J. Burt Effect of inflammatory bowel disease classification changes on NOD2 genotype-phenotype associations in a population-based cohort Inflamm Bowel Dis 13 2007 1220 1227
36. M. Mitrovič, and U. Potočnik High-resolution melting curve analysis for high-throughput genotyping of NOD2/CARD15 mutations and distribution of these mutations in Slovenian inflammatory bowel diseases patients Dis Markers 30 2011 265 274
37. J. Hampe, A. Franke, and 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
38. R.L. Roberts, R.K. Topless, and A.J. Phipps-Green Evidence of interaction of CARD8 rs2043211 with NALP3 rs35829419 in Crohn's disease Genes Immun 11 2010 351 356
39. S.K. Yang, H. Kim, and M. Hong Association of CARD8 with inflammatory bowel disease in Koreans J Hum Genet 56 2011 217 223
40. C. Huebner, L.R. Ferguson, and D.Y. Han Nucleotide-binding oligomerization domain containing 1 (NOD1) haplotypes and single nucleotide polymorphisms modify susceptibility to inflammatory bowel diseases in a New Zealand Caucasian population: a case-control study BMC Res Notes 2 2009 52
41. R. Verma, V. Ahuja, and J. Paul Frequency of single nucleotide polymorphisms in NOD1 gene of ulcerative colitis patients: a case-control study in the Indian population BMC Med Genet 10 2009 82
42. I. Petermann, C. Huebner, and B.L. Browning Interactions among genes influencing bacterial recognition increase IBD risk in a population-based New Zealand cohort Hum Immunol 70 2009 440 446
43. D. Franchimont, S. Vermeire, and H. El Housni Deficient host-bacteria interactions in inflammatory bowel disease? The toll-like receptor (TLR)-4 Asp299gly polymorphism is associated with Crohn's disease and ulcerative colitis Gut 53 2004 987 992
44. S. Schroepf, R. Kappler, and S. Brand Strong overexpression of CXCR3 axis components in childhood inflammatory bowel disease Inflamm Bowel Dis 16 2010 1882 1890
45. O. Palmieri, A. Latiano, and E. Salvatori The -A2518G polymorphism of monocyte chemoattractant protein-1 is associated with Crohn's disease Am J Gastroenterol 105 2010 1586 1594
46. S.A. Fisher, M. Tremelling, and C.A. Anderson Genetic determinants of ulcerative colitis include the ECM1 locus and five loci implicated in Crohn's disease Nat Genet 40 2008 710 712
47. J.D. Rioux, R.J. Xavier, and 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
48. A.M. Muise, T. Walters, and E. Wine Protein-tyrosine phosphatase sigma is associated with ulcerative colitis Curr Biol 17 2007 1212 1218
49. A.M. Muise, T.D. Walters, and W.K. Glowacka Polymorphisms in E-cadherin (CDH1) result in a mis-localised cytoplasmic protein that is associated with Crohn's disease Gut 58 2009 1121 1127
50. B.L. Browning, C. Huebner, and I. Petermann Association of DLG5 variants with inflammatory bowel disease in the New Zealand Caucasian population and meta-analysis of the DLG5 R30Q variant Inflamm Bowel Dis 13 2007 1069 1076
51. A.A. van Bodegraven, C.R. Curley, and K.A. Hunt Genetic variation in myosin IXB is associated with ulcerative colitis Gastroenterology 131 2006 1768 1774
52. C. Núñez, J. Oliver, and J.L. Mendoza MYO9B polymorphisms in patients with inflammatory bowel disease Gut 56 2007 1321 1322
53. A. Latiano, O. Palmieri, and M.R. Valvano The association of MYO9B gene in Italian patients with inflammatory bowel diseases Aliment Pharmacol Ther 27 2008 241 248
54. R. Cooney, J.R. Cummings, and S. Pathan Association between genetic variants in myosin IXB and Crohn's disease Inflamm Bowel Dis 15 2009 1014 1021
55. V.M. Wolters, W. Xu, and X. Zhao Replication of genetic variation in the MYO9B gene in Crohn's disease Hum Immunol 72 2011 592 597
56. J. Glas, J. Seiderer, and D. Fischer Pregnane X receptor (PXR/NR1I2) gene haplotypes modulate susceptibility to inflammatory bowel disease Inflamm Bowel Dis 17 2011 1917 1924
57. R.W. Bentley, I. Cleynen, and R.B. Gearry Evidence that glioma-associated oncogene homolog 1 is not a universal risk gene for inflammatory bowel disease in Caucasians Genes Immun 11 2010 509 514
58. V.D. Peltekova, R.F. Wintle, and L.A. Rubin Functional variants of OCTN cation transporter genes are associated with Crohn disease Nat Genet 36 2004 471 475
59. M. Zucchelli, L. Torkvist, and F. Bresso PepT1 oligopeptide transporter (SLC15A1) gene polymorphism in inflammatory bowel disease Inflamm Bowel Dis 15 2009 1562 1569
60. L.C. Stewart, A.S. Day, and J. Pearson SLC11A1 polymorphisms in inflammatory bowel disease and Mycobacterium avium subspecies paratuberculosis status World J Gastroenterol 16 2010 5727 5731
61. C. Huebner, B.L. Browning, and I. Petermann Genetic analysis of MDR1 and inflammatory bowel disease reveals protective effect of heterozygous variants for ulcerative colitis Inflamm Bowel Dis 15 2009 1784 1793
62. J.J. Eloranta, C. Wenger, and J. Mwinyi Association of a common vitamin D-binding protein polymorphism with inflammatory bowel disease Pharmacogenet Genomics 21 2011 559 564
63. U.K. Shrestha, O. Karimi, and J.B. Crusius Distribution of peroxisome proliferator-activated receptor-gamma polymorphisms in Chinese and Dutch patients with inflammatory bowel disease Inflamm Bowel Dis 16 2010 312 319
64. L.A. Simms, J.D. Doecke, and R.L. Roberts KCNN4 gene variant is associated with ileal Crohn's Disease in the Australian and New Zealand population Am J Gastroenterol 105 2010 2209 2217
65. A. Márquez, C. Núñez, and A. Martínez Role of ATG16L1 Thr300Ala polymorphism in inflammatory bowel disease: a study in the Spanish population and a meta-analysis Inflamm Bowel Dis 15 2009 1697 1704
66. K. Fellermann, D.E. Stange, and E. Schaeffeler A chromosome 8 gene-cluster polymorphism with low human beta-defensin 2 gene copy number predisposes to Crohn disease of the colon Am J Hum Genet 79 2006 439 448
67. L.R. Ferguson, B.L. Browning, and C. Huebner Single nucleotide polymorphisms in human Paneth cell defensin A5 may confer susceptibility to inflammatory bowel disease in a New Zealand Caucasian population Dig Liver Dis 40 2008 723 730
68. Z. Lin, G. John, and J.P. Hegarty Genetic variants and monoallelic expression of Surfactant Protein-D in inflammatory bowel disease Ann Hum Genet 75 2011 559 568
69. D.K. Amre, D.R. Mack, and K. Morgan Investigation of reported associations between the 20q13 and 21q22 loci and pediatric-onset Crohn's disease in Canadian children Am J Gastroenterol 104 2009 2824 2828
70. D.A. van Heel, S.A. Fisher, and A. Kirby Inflammatory bowel disease susceptibility loci defined by genome scan meta-analysis of 1952 affected relative pairs Hum Mol Genet 13 2004 763 770
71. P.C. Stokkers, P.H. Reitsma, G.N. Tytgat, and S.J. van Deventer HLA-DR and -DQ phenotypes in inflammatory bowel disease: a meta-analysis Gut 45 1999 395 401
72. A.M. Valdes, U. Styrkarsdottir, and M. Doherty Large scale replication study of the association between HLA class II/BTNL2 variants and osteoarthritis of the knee in European-descent populations PLoS One 6 2011 e23371
73. M.T. Abreu, K.D. Taylor, and Y.C. Lin Mutations in NOD2 are associated with fibrostenosing disease in patients with Crohn's disease Gastroenterology 123 2002 679 688
74. A. Karban, M. Waterman, and C.I. Panhuysen NOD2/CARD15 genotype and phenotype differences between Ashkenazi and Sephardic Jews with Crohn's disease Am J Gastroenterol 99 2004 1134 1140
75. H.H. Fidder, B. Avidan, M. Lahav, S. Bar-Meir, and Y. Chowers Clinical and demographic characterization of Jewish Crohn's disease patients in Israel J Clin Gastroenterol 36 2003 8 12
76. B.L. Browning, C. Huebner, and I. Petermann Has toll-like receptor 4 been prematurely dismissed as an inflammatory bowel disease gene? Association study combined with meta-analysis shows strong evidence for association Am J Gastroenterol 102 2007 2504 2512
77. A. Franke, D.P. McGovern, and 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
78. M.A. Rivas, M. Beaudoin, and A. Gardet Deep resequencing of GWAS loci identifies independent rare variants associated with inflammatory bowel disease Nat Genet 43 2011 1066 1073
79. E. Mainardi, V. Villanacci, and G. Bassotti Diagnostic value of serological assays in pediatric inflammatory bowel disorders Digestion 75 2007 210 214