A genome-wide association scan of nonsynonymous SNPs identifies a susceptibility variant for Crohn disease in ATG16L1

Nature Genetics

Volumn 39, Issue 2, 2007, Pages 207-211

  Hampe, Jochen ^a   Franke, Andre ^a   Rosenstiel, Philip ^a,f   Till, Andreas ^a   Teuber, Markus ^a   Huse, Klaus ^b   Albrecht, Mario ^c   Mayr, Gabriele ^c   De La Vega, Francisco M ^d   Briggs, Jason ^d   Günther, Simone ^d   Prescott, Natalie J ^e   Onnie, Clive M ^e   Häsler, Robert ^a   Sipos, Bence ^a   Fölsch, Ulrich R ^a   Lengauer, Thomas ^c   Platzer, Matthias ^b   Mathew, Christopher G ^e   Krawczak, Michael ^a   Schreiber, Stefan ^a   more..

^a UNIVERSITY OF KIEL   (Germany)

^b FRITZ LIPMANN INSTITUTE   (Germany)

^c MAX PLANCK INSTITUTE FOR INFORMATICS   (Germany)

^d APPLIED BIOSYSTEMS   (United States)

^e KING'S COLLEGE LONDON   (United Kingdom)

^f MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; ARTICLE; ATG16L1 GENE; AUTOPHAGY; BACTERIUM; CONTROLLED STUDY; CROHN DISEASE; DISEASE ASSOCIATION; FOLLOW UP; GENE; GENE LOCUS; GENE REPLICATION; GENOME; HAPLOTYPE; HUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; REGRESSION ANALYSIS; RISK; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL SIGNIFICANCE; ULCERATIVE COLITIS;

CARRIER PROTEINS; CROHN DISEASE; GENETIC PREDISPOSITION TO DISEASE; HUMANS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NOD2 SIGNALING ADAPTOR PROTEIN; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 33846627302     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng1954     Document Type: Article

References (30)

1. Hugot, J.P. et al. Association of NOD2 leucine-rich repeat variants with susceptibility to Crohn's disease. Nature 411, 599-603 (2001).
2. Ogura, Y. et al. A frameshift mutation in NOD2 associated with susceptibility to Crohn's disease. Nature 411, 603-606 (2001).
3. Rioux, J.D. et al. Genetic variation in the 5q31 cytokine gene cluster confers susceptibility to Crohn disease. Nat. Genet. 29, 223-228 (2001).
4. Peltekova, V.D. et al. Functional variants of OCTN cation transporter genes are associated with Crohn disease. Nat. Genet. 36, 471-475 (2004).
5. Stoll, M. et al. Genetic variation in DLG5 is associated with inflammatory bowel disease. Nat. Genet. 36, 476-480 (2004).
6. Brant, S.R. et al. MDR1 Ala893 polymorphism is associated with inflammatory bowel disease. Am. J. Hum. Genet. 73, 1282-1292 (2003).
7. Ho, G.T. et al. ABCB1/MDR1 gene determines susceptibility and phenotype in ulcerative colitis: discrimination of critical variants using a gene-wide haplotype tagging approach. Hum. Mol. Genet. 15, 797-805 (2006).
8. Schwab, M. et al. Association between the C3435T MDR1 gene polymorphism and susceptibility for ulcerative colitis. Gastroenterology 124, 26-33 (2003).
9. McGovern, D.P. et al. Association between a complex insertion/deletion polymorphism in NOD1 (CARD4) and susceptibility to inflammatory bowel disease. Hum. Mol. Genet. 14, 1245-1250 (2005).
10. Yamazaki, K. et al. Single nucleotide polymorphisms in TNFSF15 confer susceptibility to Crohn's disease. Hum. Mol. Genet. 14, 3499-3506 (2005).
11. Duerr, R.H. et al. A genome-wide association study identifies IL23R as an inflammatory bowel disease gene. Science 314, 1461-1463 (2006).
12. Maeda, S. et al. Nod2 mutation in Crohn's disease potentiates NF-kappaB activity and IL-1beta processing. Science 307, 734-738 (2005).
13. Kobayashi, K.S. et al. Nod2-dependent regulation of innate and adaptive immunity in the intestinal tract. Science 307, 731-734 (2005).
14. Girardin, S.E. et al. Nod2 is a general sensor of peptidoglycan through muramyl dipeptide (MDP) detection. J. Biol. Chem. 278, 8869-8872 (2003).
15. Hampe, J. et al. Association between insertion mutation in NOD2 gene and Crohn's disease in German and British populations. Lancet 357, 1925-1928 (2001).
16. Watanabe, T., Kitani, A., Murray, P.J. & Strober, W. NOD2 is a negative regulator of Toll-like receptor 2-mediated T helper type 1 responses. Nat. Immunol. 5, 800-808 (2004).
17. Smyth, D.J. et al. A genome-wide association study of nonsynonymous SNPs identifies a type 1 diabetes locus in the interferon-induced helicase (IFIH1) region. Nat. Genet. 38, 617-619 (2006).
18. Duerr, R.H., Barmada, M.M., Zhang, L., Pfutzer, R. & Weeks, D.E. High-density genome scan in Crohn disease shows confirmed linkage to chromosome 14q11-12. Am. J. Hum. Genet. 66, 1857-1862 (2000).
19. Hampe, J. et al. A genome-wide analysis provides evidence for novel linkages in inflammatory bowel disease in a large European cohort. Am. J. Hum. Genet. 64, 808-816 (1999).
20. Shaw, S.H. et al. Stratification by CARD15 variant genotype in a genome-wide search for inflammatory bowel disease susceptibility loci. Hum. Genet. 113, 514-521 (2003).
21. Croucher, P.J.P. et al. Haplotype structure and association to Crohn's disease of CARD15 mutations in two ethnically divergent populations. Eur. J. Hum. Genet. 11, 6-16 (2003).
22. Zheng, H. et al. Cloning and analysis of human Apg16L. DNA Seq. 15, 303-305 (2004).
23. Mizushima, N. et al. Mouse Apg16L, a novel WD-repeat protein, targets to the autophagic isolation membrane with the Apg12-Apg5 conjugate. J. Cell Sci. 116, 1679-1688 (2003).
24. Hampe, J. et al. An integrated system for high throughput TaqMan based SNP genotyping. Bioinformatics 17, 654-655 (2001).
25. Hampe, J. et al. Evidence for a NOD2-independent susceptibility locus for inflammatory bowel disease on chromosome 16p. Proc. Natl. Acad. Sci. USA 99, 321-326 (2002).
26. Venter, J.C. et al. The sequence of the human genome. Science 291, 1304-1351 (2001).
27. Manaster, C. et al. InSNP: a tool for automated detection and visualization of SNPs and InDels. Hum. Mutat. 26, 11-19 (2005).
28. Barrett, J.C., Fry, B., Maller, J. & Daly, M.J. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21, 263-265 (2005).
29. Franke, A. et al. GENOMIZER: an integrated analysis system for genome-wide association data. Hum. Mutat. 27, 583-588 (2006).
30. Dudbridge, F. Pedigree disequilibrium tests for multilocus haplotypes. Genet. Epidemiol. 25, 115-121 (2003).