Replication study of ulcerative colitis risk loci in a lithuanian latvian case control sample

Inflammatory Bowel Diseases

Volumn 19, Issue 11, 2013, Pages 2349-2355

  Skieceviciene, Jurgita ^a   Kiudelis, Gediminas ^a   Ellinghaus, Eva ^b   Balschun, Tobias ^b   Jonaitis, Laimas V ^a   Zvirbliene, Aida ^a   Denapiene, Goda ^c   Leja, Marcis ^d   Pranculiene, Gitana ^a   Kalibatas, Vytenis ^a   Saadati, Hamidreza ^b   Ellinghaus, David ^b   Andersen, Vibeke ^e,f   Valantinas, Jonas ^c   Irnius, Algimantas ^c   Derovs, Aleksejs ^g   Tamelis, Algimantas ^a   Schreiber, Stefan ^b   Kupcinskas, Limas ^a   Franke, Andre ^b  

^a LITHUANIAN UNIVERSITY OF HEALTH SCIENCES   (Lithuania)

^b UNIVERSITY OF KIEL   (Germany)

^c VILNIUS UNIVERSITY   (Lithuania)

^d Digestive Diseases Centre GASTRO   (Latvia)

^e UNIVERSITY OF SOUTHERN DENMARK   (Denmark)

^f Hospital of Southern Jutland   (Denmark)

^g RIGA STRADINS UNIVERSITY   (Latvia)

Author keywords

Case control; Lithuanian Latvian; Single nucleotide polymorphisms; Ulcerative colitis

Indexed keywords

INTERLEUKIN 10; INTERLEUKIN 23 RECEPTOR; JANUS KINASE 2;

ADULT; ALLELE; ARTICLE; C13ORF31 GENE; CHROMOSOME 1P; CHROMOSOME 21Q; CONTROLLED STUDY; CROHN DISEASE; EPISTASIS; GENE LOCUS; GENOTYPE; HUMAN; MAJOR CLINICAL STUDY; MST1 GENE; NKX2-3 GENE; ORMDL3 GENE; PRIORITY JOURNAL; PTPN22 GENE; SINGLE NUCLEOTIDE POLYMORPHISM; ULCERATIVE COLITIS;

ADULT; BIOLOGICAL MARKERS; CASE-CONTROL STUDIES; COLITIS, ULCERATIVE; EUROPE; FEMALE; FOLLOW-UP STUDIES; GENETIC PREDISPOSITION TO DISEASE; GENOME-WIDE ASSOCIATION STUDY; HUMANS; MALE; POLYMORPHISM, SINGLE NUCLEOTIDE; PROGNOSIS; PROTEIN TYROSINE PHOSPHATASE, NON-RECEPTOR TYPE 22; RISK FACTORS;

EID: 84888263784     PISSN: 10780998     EISSN: 15364844     Source Type: Journal    
DOI: 10.1097/MIB.0b013e3182a3eaeb     Document Type: Article

References (52)

1. Loftus EV. Clinical epidemiology of inflammatory bowel disease: Incidence, prevalence, and environmental influences. Gastroenterology. 2004; 126:1504-1517.
2. Burisch J, Pedersen N, Cukovic-Cavka S, et al. East-West gradient in the incidence of inflammatory bowel disease in Europe: the ECCO-EpiCom inception cohort. Gut. [published online ahead of print April 20, 2013]. doi: 10.1136/gutjnl-2013-304636.
3. Cooney R, Jewell D. The genetic basis of inflammatory bowel disease. Dig Dis. 2009;27:428-442.
4. Jostins L, Ripke S, Weersma RK, et al. Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. Nature. 2012;491:119-124.
5. Moore JH. A global view of epistasis. Nat Genet. 2005;37:13-14.
6. Cordell HJ. Detecting gene-gene interactions that underlie human diseases. Nat Rev Genet. 2009;10:392-404.
7. Moore JH. The ubiquitous nature of epistasis in determining susceptibility to common human diseases. Hum Hered. 2003;56:73-82.
8. Franke A, McGovern DPB, Barrett JC, et al. Genome-wide meta-analysis increases to 71 the number of confirmed Crohns disease susceptibility loci. Nat Genet. 2010;42:1118-1125.
9. McGovern DPB, Gardet A, Törkvist L, et al. Genome-wide association identifies multiple ulcerative colitis susceptibility loci. Nat Genet. 2010; 42:332-337.
10. Wellcome Trust Case Control Consortium. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature. 2007;447:661-678.
11. Barrett JC, Lee JC, Lees CW, et al. Genome-wide association study of ulcerative colitis identifies three new susceptibility loci, including the HNF4A region. Nat Genet. 2009;41:1330-1334.
12. Evans DM, Spencer CC, Pointon JJ, et al. Interaction between ERAP1 and HLA-B27 in ankylosing spondylitis implicates peptide handling in the mechanism for HLA-B27 in disease susceptibility. Nat Genet. 2011;43:761-767.
13. Strange A, Capon F, Spencer CC, et al. A genome-wide association study identifies new psoriasis susceptibility loci and an interaction between HLA-C and ERAP1. Nat Genet. 2010;42:985-990.
14. Barrett JC, Clayton DG, Concannon P, et al. Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes. Nat Genet. 2009;41:703-707.
15. Anderson CA, Boucher G, Lees CW, et al. Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to Nat Genet. 2011;43:246-252.
16. Podolsky DK. Inflammatory bowel disease (1). N Engl J Med. 1991;325: 928-937.
17. Sventoraityte J, Zvirbliene A, Franke A, et al. NOD2, IL23R and ATG16L1 polymorphisms in Lithuanian patients with inflammatory bowel disease. World J Gastroenterol. 2010;16:359-364.
18. Silverberg MS, Satsangi J, Ahmad T, et al. Toward an integrated clinical, molecular and serological classification of inflammatory bowel disease: report of a working party of the 2005 montreal world congress of gastroenterology. Can J Gastroenterol. 2005;19(suppl A):5-36.
19. Andersen V, Ernst A, Sventoraityte J, et al. Assessment of heterogeneity between European Populations: A Baltic and Danish replication casecontrol study of SNPs from a recent European ulcerative colitis genome wide association study. BMC Med Genet. 2011;12:139.
20. Franke A, Balschun T, Karlsen TH, et al. Sequence variants in IL10, ARPC2 and multiple other loci contribute to ulcerative colitis susceptibility. Nat Genet. 2008;40:1319-1323.
21. Franke A, Balschun T, Sina C, et al. Genome-wide association study for ulcerative colitis identifies risk loci at 7q22 and 22q13 (IL17REL). Nat Genet. 2010;42:292-294.
22. Franke A, Hampe J, Rosenstiel P, et al. Systematic association mapping identifies NELL1 as a novel IBD disease gene. PLoS One. 2007;2:e691.
23. Parkes M, Barrett JC, Prescott NJ, et al. Sequence variants in the autophagy gene IRGM and multiple other replicating loci contribute to Crohns disease susceptibility. Nat Genet. 2007;39:830-832.
24. Barrett JC, Hansoul S, Nicolae DL, et al. Genome-wide association defines more than 30 distinct susceptibility loci for Crohns disease. Nat Genet. 2008;40:955-962.
25. Silverberg MS, Cho JH, Rioux JD, et al. Ulcerative colitis-risk loci on chromosomes 1p36 and 12q15 found by genome-wide association study. Nat Genet. 2009;41:216-220.
26. Ogura Y, Bonen DK, Inohara N, et al. A frameshift mutation in NOD2 associated with susceptibility to Crohns disease. Nature. 2001;411:603-606.
27. Hugot JP, Chamaillard M, Zouali H, et al. Association of NOD2 leucinerich repeat variants with susceptibility to Crohns disease. Nature. 2001; 411:599-603.
28. Stoll M, Corneliussen B, Costello CM, et al. Genetic variation in DLG5 is associated with inflammatory bowel disease. Nat Genet. 2004;36:476-480.
29. Duerr RH, Taylor KD, Brant SR, et al. A genome-wide association study identifies IL23R as an inflammatory bowel disease gene. Science. 2006; 314:1461-1463.
30. Peltekova VD, Wintle RF, Rubin LA, et al. Functional variants of OCTN cation transporter genes are associated with Crohn disease. Nat Genet. 2004;36:471-475.
31. Yamazaki K, McGovern D, Ragoussis J, et al. Single nucleotide polymorphisms in TNFSF15 confer susceptibility to Crohns disease. Hum Mol Genet. 2005;14:3499-3506.
32. Libioulle C, Louis E, Hansoul S, et al. Novel Crohn disease locus identified by genome-wide association maps to a gene desert on 5p13.1 and modulates expression of PTGER4. PLoS Genet. 2007;3:e58.
33. Raelson J V, Little RD, Ruether A, et al. Genome-wide association study for Crohns disease in the Quebec Founder Population identifies multiple validated disease loci. Proc Natl Acad Sci U S A. 2007;104:14747-14752.
34. 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;39:207-211.
35. Purcell S, Neale B, Todd-Brown K, et al. PLINK: A tool set for wholegenome association and population-based linkage analyses. Am J Hum Genet. 2007;81:559-575.
36. Nelis M, Esko T, Mägi R, et al. Genetic structure of Europeans: A view from the North-East. PLoS One. 2009;4:e5472.
37. Fisher SA, Tremelling M, Anderson CA, et al. Genetic determinants of ulcerative colitis include the ECM1 locus and five loci implicated in Crohns disease. Nat Genet. 2008;40:710-712.
38. Franke A, Balschun T, Karlsen TH, et al. Replication of signals from recent studies of Crohns disease identifies previously unknown disease loci for ulcerative colitis. Nat Genet. 2008;40:713-715.
39. Törkvist L, Halfvarson J, Ong RTH, et al. Analysis of 39 Crohns disease risk loci in Swedish inflammatory bowel disease patients. Inflamm Bowel Dis. 2010;16:907-909.
40. Wang K, Baldassano R, Zhang H, et al. Comparative genetic analysis of inflammatory bowel disease and type 1 diabetes implicates multiple loci with opposite effects. Hum Mol Genet. 2010;19:2059-2067.
41. Festen EAM, Stokkers PCF, van Diemen CC, et al. Genetic analysis in a Dutch study sample identifies more ulcerative colitis susceptibility loci and shows their additive role in disease risk. Am J Gastroenterol. 2010;105:395-402.
42. Andersen V, Ernst A, Christensen J, et al. The polymorphism rs3024505 proximal to IL-10 is associated with risk of ulcerative colitis and Crohns disease in a Danish case-control study. BMC Med Genet. 2010;11:82.
43. Glas J, Seiderer J, Wagner J, et al. Analysis of IL12B gene variants in inflammatory bowel disease. PLoS One. 2012;7:e34349.
44. Torok HP, Glas J, Endres I, et al. Epistasis between Toll-like receptor-9 polymorphisms and variants in NOD2 and IL23R modulates susceptibility to Crohns disease. Am J Gastroenterol. 2009;104:1723-1733.
45. Glas J, Seiderer J,Wetzke M, et al. rs1004819 is the main disease-associated IL23R variant in German Crohns disease patients: combined analysis of IL23R, CARD15, and OCTN1/2 variants. PLoS One. 2007;2:e819.
46. Glas J, Konrad A, Schmechel S, et al. The ATG16L1 gene variants rs2241879 and rs2241880 (T300A) are strongly associated with susceptibility to Crohns disease in the German population. Am J Gastroenterol. 2008;103:682-691.
47. Lee YH, Rho YH, Choi SJ, et al. The PTPN22 C1858T functional polymorphism and autoimmune diseases-a meta-analysis. Rheumatology (Oxford). 2007;46:49-56.
48. Zhang FR, Huang W, Chen SM, et al. Genomewide association study of leprosy. N Engl J Med. 2009;361:2609-2618.
49. Stanford SM, Mustelin TM, Bottini N. Lymphoid tyrosine phosphatase and autoimmunity: human genetics rediscovers tyrosine phosphatases. Semin Immunopathol. 2010;32:127-136.
50. Rieck M, Arechiga A, Onengut-Gumuscu S, et al. Genetic variation in PTPN22 corresponds to altered function of T and B lymphocytes. J Immunol. 2007;179:4704-4710.
51. Vang T, Congia M, Macis MD, et al. Autoimmune-associated lymphoid tyrosine phosphatase is a gain-of-function variant. Nat Genet. 2005;37: 1317-1319.
52. Hasegawa K, Martin F, Huang G, et al. PEST domain-enriched tyrosine phosphatase (PEP) regulation of effector/memory T cells. Science. 2004; 303:685-689.