Deep resequencing of 131 Crohn's disease associated genes in pooled DNA confirmed three reported variants and identified eight novel variants

Gut

Volumn 65, Issue 5, 2016, Pages 788-796

  Hong, Sung Noh ^a   Park, Changho ^b   Park, Soo Jung ^c   Lee, Chang Kyun ^d   Ye, Byong Duk ^e   Kim, You Sun ^f   Lee, Seungbok ^b   Chae, Jeesoo ^b   Kim, Jong Il ^b   Kim, Young Ho ^a  

^a Samsung Medical Center   (South Korea)

^b Seoul National University   (South Korea)

^c Yonsei University College of Medicine   (South Korea)

^d Kyung Hee University Hospital   (South Korea)

^e Asan Medical Center   (South Korea)

^f Inje University College of Medicine   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

STAT3 PROTEIN;

ADULT; ARTICLE; ATG16L1 GENE; BTNL2 GENE; CARD9 GENE; CONTROLLED STUDY; CROHN DISEASE; DNAH12 GENE; EXON; GENE; GENE IDENTIFICATION; GENE LOCUS; GENE SEQUENCE; GENETIC ASSOCIATION; GENETIC VARIABILITY; HLA DQA2 GENE; HUMAN; IL23R GENE; KOREAN (PEOPLE); MAJOR CLINICAL STUDY; NFKBIA GENE; NKX2 GENE; NKX3 GENE; PRIORITY JOURNAL; STAT3 GENE; TNFSF15 GENE; TNFSF8 GENE; DNA SEQUENCE; GENETIC VARIATION; GENETICS; HIGH THROUGHPUT SEQUENCING;

CROHN DISEASE; GENETIC VARIATION; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; SEQUENCE ANALYSIS, DNA;

EID: 84929589668     PISSN: 00175749     EISSN: 14683288     Source Type: Journal    
DOI: 10.1136/gutjnl-2014-308617     Document Type: Article

References (61)

1. Liu JZ, Anderson CA. Genetic studies of Crohn's disease: past, present and future. Best Pract Res Clin Gastroenterol 2014;28:373-86.
2. Yang SK, Hong M, Zhao W, et al. Genome-wide association study of Crohn's disease in Koreans revealed three new susceptibility loci and common attributes of genetic susceptibility across ethnic populations. Gut 2014;63:80-7.
3. Liu Y, Xu H, Chen S, et al. Genome-wide interaction-based association analysis identified multiple new susceptibility loci for common diseases. PLoS Genet 2011;7:e1001338.
4. Rivas MA, Beaudoin M, Gardet A, et al. Deep resequencing of GWAS loci identifies independent rare variants associated with inflammatory bowel disease. Nat Genet 2011;43:1066-73.
5. Out AA, van Minderhout IJ, Goeman JJ, et al. Deep sequencing to reveal new variants in pooled DNA samples. Hum Mutat 2009;30:1703-12.
6. Ng SC, Tsoi KK, Kamm MA, et al. Genetics of inflammatory bowel disease in Asia: systematic review and meta-analysis. Inflamm Bowel Dis 2012;18:1164-76.
7. Inoue N, Tamura K, Kinouchi Y, et al. Lack of common NOD2 variants in Japanese patients with Crohn's disease. Gastroenterology 2002;123:86-91.
8. Leong RW, Armuzzi A, Ahmad T, et al. NOD2/CARD15 gene polymorphisms and Crohn's disease in the Chinese population. Aliment Pharmacol Ther 2003;17:1465-70.
9. 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.
10. Yang SK, Park M, Lim J, et al. Contribution of IL23R but not ATG16L1 to Crohn's disease susceptibility in Koreans. Inflamm Bowel Dis 2009;15:1385-90.
11. Picornell Y, Mei L, Taylor K, et al. TNFSF15 is an ethnic-specific IBD gene. Inflamm Bowel Dis 2007;13:1333-8.
12. Yang SK, Lim J, Chang HS, et al. Association of TNFSF15 with Crohn's disease in Koreans. Am J Gastroenterol 2008;103:1437-42.
13. Ogura Y, Bonen DK, Inohara N, et al. A frameshift mutation in NOD2 associated with susceptibility to Crohn's disease. Nature 2001;411:603-6.
14. Hugot JP, Chamaillard M, Zouali H, et al. Association of NOD2 leucine-rich repeat variants with susceptibility to Crohn's disease. Nature 2001;411:599-603.
15. Lee GH, Kim CG, Kim JS, et al. Frequency analysis of NOD2 gene mutations in Korean patients with Crohn's disease. Korean J Gastroenterol 2005;45:162-8.
16. Glas J, Konrad A, Schmechel S, et al. The ATG16L1 gene variants rs2241879 and rs2241880 (T300A) are strongly associated with susceptibility to Crohn's disease in the German population. Am J Gastroenterol 2008;103:682-91.
17. Yang SK, Ye BD, Song K. ATG16L1 contributes to Crohn's disease susceptibility in Koreans: overmuch concern for ethnic difference? Gut 2015;64:687-8.
18. Duerr RH, Taylor KD, Brant SR, et al. A genome-wide association study identifies IL23R as an inflammatory bowel disease gene. Science 2006;314:1461-3.
19. Kim SW, Kim ES, Moon CM, et al. Genetic polymorphisms of IL-23R and IL-17A and novel insights into their associations with inflammatory bowel disease. Gut 2011;60:1527-36.
20. Chen GB, Lee SH, Brion MJ, et al. Estimation and partitioning of (co) heritability of inflammatory bowel disease from GWAS and immunochip data. Hum Mol Genet 2014;23:4710-20.
21. Cheon JH, Kim YS, Ye BD, et al. Crohn's Disease Clinical Network and Cohort (CONNECT) Study: The first step toward nationwide multicenter research of Crohn's disease in Korea. Intest Res 2014;12:173-5.
22. Ye BD, Jang BI, Jeen YT, et al. Diagnostic guideline of Crohn's disease. Korean J Gastroenterol 2009;53:161-76.
23. Hong SN, Park CH, Kim JI, et al. Colorectal cancer-susceptibility single nucleotide polymorphisms in Korean population. J Gastroenterol Hepatol 2013. Jul. 22. DOI: 10.1111/jgh.12331.
24. Rioux JD, Daly MJ, Silverberg MS, et al. Genetic variation in the 5q31 cytokine gene cluster confers susceptibility to Crohn disease. Nat Genet 2001;29:223-8.
25. Stoll M, Corneliussen B, Costello CM, et al. Genetic variation in DLG5 is associated with inflammatory bowel disease. Nat Genet 2004;36:476-80.
26. Franchimont D, Vermeire S, El Housni H, et al. 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 2004;53:987-92.
27. Parkes M, Barrett JC, Prescott NJ, et al. Sequence variants in the autophagy gene IRGM and multiple other replicating loci contribute to Crohn's disease susceptibility. Nat Genet 2007;39:830-2.
28. Momozawa Y, Mni M, Nakamura K, et al. Resequencing of positional candidates identifies low frequency IL23R coding variants protecting against inflammatory bowel disease. Nat Genet 2011;43:43-7.
29. Hampe J, Franke A, Rosenstiel P, et al. A genome-wide association scan of nonsynonymous SNPs identifies a susceptibility variant for Crohn disease in ATG16L1. Nat Genet 2007;39:207-11.
30. Weersma RK, Stokkers PC, Cleynen I, et al. Confirmation of multiple Crohn's disease susceptibility loci in a large Dutch-Belgian cohort. Am J Gastroenterol 2009;104:630-8.
31. Rioux JD, Xavier RJ, Taylor KD, et al. Genome-wide association study identifies new susceptibility loci for Crohn disease and implicates autophagy in disease pathogenesis. Nat Genet 2007;39:596-604.
32. Henckaerts L, Cleynen I, Brinar M, et al. Genetic variation in the autophagy gene ULK1 and risk of Crohn's disease. Inflamm Bowel Dis 2011;17:1392-7.
33. 1502 haplotype increases risk for ulcerative colitis but reduces risk for Crohn's disease. Gastroenterology 2011;141:864-871.e1-5.
34. Barrett JC, Hansoul S, Nicolae DL, et al. Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease. Nat Genet 2008;40:955-62.
35. Nakagome S, Takeyama Y, Mano S, et al. Population-specific susceptibility to Crohn's disease and ulcerative colitis; dominant and recessive relative risks in the Japanese population. Ann Hum Genet 2010;74:126-36.
36. van der Heide F, Nolte IM, Kleibeuker JH, et al. Differences in genetic background between active smokers, passive smokers, and non-smokers with Crohn's disease. Am J Gastroenterol 2010;105:1165-72.
37. Franke A, McGovern DP, Barrett JC, et al. Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci. Nat Genet 2010;42:1118-25.
38. Festen EA, Goyette P, Green T, et al. A meta-analysis of genome-wide association scans identifies IL18RAP, PTPN2, TAGAP, and PUS10 as shared risk loci for Crohn's disease and celiac disease. PLoS Genet 2011;7:e1001283.
39. Umeno J, Asano K, Matsushita T, et al. Meta-analysis of published studies identified eight additional common susceptibility loci for Crohn's disease and ulcerative colitis. Inflamm Bowel Dis 2011;17:2407-15.
40. Fransen K, Visschedijk MC, van Sommeren S, et al. Analysis of SNPs with an effect on gene expression identifies UBE2L3 and BCL3 as potential new risk genes for Crohn's disease. Hum Mol Genet 2010;19:3482-8.
41. Yu W, Gwinn M, Clyne M, et al. A navigator for human genome epidemiology. Nat Genet 2008;40:124-5.
42. Zhang J, Zhang J, Wu D, et al. Associations between TNFSF15 polymorphisms and susceptibility to ulcerative colitis and Crohn's disease: a meta-analysis. Autoimmunity 2014;47:512-18.
43. Lui VW, Peyser ND, Ng PK, et al. Frequent mutation of receptor protein tyrosine phosphatases provides a mechanism for STAT3 hyperactivation in head and neck cancer. Proc Natl Acad Sci USA 2014;111:1114-19.
44. Mitsunaga S, Hosomichi K, Okudaira Y, et al. Exome sequencing identifies novel rheumatoid arthritis-susceptible variants in the BTNL2. J Hum Genet 2013;58:210-15.
45. Murthy A, Li Y, Peng I, et al. A Crohn's disease variant in Atg16l1 enhances its degradation by caspase 3. Nature 2014;506:456-62.
46. Arai T, Kakuta Y, Kinouchi Y, et al. Increased expression of NKX2.3 mRNA transcribed from the risk haplotype for ulcerative colitis in the involved colonic mucosa. Hum Immunol 2011;72:587-91.
47. Sims D, Sudbery I, Ilott NE, et al. Sequencing depth and coverage: key considerations in genomic analyses. Nat Rev Genet 2014;15:121-32.
48. Sun X, Shibata K, Yamada H, et al. CD30L/CD30 is critical for maintenance of IL-17A-producing gammadelta T cells bearing Vgamma6 in mucosa-associated tissues in mice. Mucosal Immunol 2013;6:1191-201.
49. Zinovieva E, Kadi A, Letourneur F, et al. Systematic candidate gene investigations in the SPA2 locus (9q32) show an association between TNFSF8 and susceptibility to spondylarthritis. Arthritis Rheum 2011;63:1853-9.
50. Johnson CM, Traherne JA, Jamieson SE, et al. Analysis of the BTNL2 truncating splice site mutation in tuberculosis, leprosy and Crohn's disease. Tissue Antigens 2007;69:236-41.
51. Valentonyte R, Hampe J, Huse K, et al. Sarcoidosis is associated with a truncating splice site mutation in BTNL2. Nat Genet 2005;37:357-64.
52. International MHC and Autoimmunity Genetics Network, Rioux JD, et al. Mapping of multiple susceptibility variants within the MHC region for 7 immune-mediated diseases. Proc Natl Acad Sci USA 2009;106:18680-5.
53. Wang Z, Xu B, Zhang H, et al. Association between STAT3 gene polymorphisms and Crohn's disease susceptibility: a case-control study in a Chinese Han population. Diagn Pathol 2014;9:104.
54. Klein W, Tromm A, Folwaczny C, et al. A polymorphism of the NFKBIA gene is associated with Crohn's disease patients lacking a predisposing allele of the CARD15 gene. Int J Colorectal Dis 2004;19:153-6.
55. Sun XF, Zhang H. NFKB and NFKBI polymorphisms in relation to susceptibility of tumour and other diseases. Histol Histopathol 2007;22:1387-98.
56. Gross O, Gewies A, Finger K, et al. Card9 controls a non-TLR signalling pathway for innate anti-fungal immunity. Nature 2006;442:651-6.
57. Kim ES, Kim WH. Inflammatory bowel disease in Korea: epidemiological, genomic, clinical, and therapeutic characteristics. Gut Liver 2010;4:1-14.
58. Gewirtz AT, Vijay-Kumar M, Brant SR, et al. Dominant-negative TLR5 polymorphism reduces adaptive immune response to flagellin and negatively associates with Crohn's disease. Am J Physiol Gastrointest Liver Physiol 2006;290:G1157-63.
59. 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.
60. Julia A, Domenech E, Ricart E, et al. A genome-wide association study on a southern European population identifies a new Crohn's disease susceptibility locus at RBX1-EP300. Gut 2013;62:1440-5.
61. Wellcome Trust Case Control C. Genome-wide association study of 14, 000 cases of seven common diseases and 3, 000 shared controls. Nature 2007;447:661-78.