Independent and population-specific association of risk variants at the IRGM locus with Crohn&#039;s disease

Prescott, N. J.; Dominy, K. M.; Kubo, Michiaki; Lewis, C. M.; Fisher, S. A.; Redon, Richard; Huang, Ni; Stranger, B. E.; Blaszczyk, Katarzyna; Hudspith, Barry; Parkes, Gareth; Hosono, Naoya; Yamazaki, Keiko; Onnie, C. M.; Forbes, Alastair; Dermitzakis, Emmanouil; Nakamura, Yusuke; Mansfield, J. C.; Sanderson, Jeremy; Hurles, M. E.; Roberts, R. G.; Mathew, C. G.

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Title		Independent and population-specific association of risk variants at the IRGM locus with Crohn's disease
Authors		Prescott, N. J. Dominy, K. M. Kubo, Michiaki Lewis, C. M. Fisher, S. A. Redon, Richard Huang, Ni Stranger, B. E. Blaszczyk, Katarzyna Hudspith, Barry Parkes, Gareth Hosono, Naoya Yamazaki, Keiko Onnie, C. M. Forbes, Alastair Dermitzakis, Emmanouil Nakamura, Yusuke Mansfield, J. C. Sanderson, Jeremy Hurles, M. E. Roberts, R. G. Mathew, C. G. show all authors [1 - 22]
Published in		Human Molecular Genetics. 2010, vol. 19, no. 9, p. 1828-1839
Abstract		DNA polymorphisms in a region on chromosome 5q33.1 which contains two genes, immunity related GTPase related family, M (IRGM) and zinc finger protein 300 (ZNF300), are associated with Crohn's disease (CD). The deleted allele of a 20 kb copy number variation (CNV) upstream of IRGM was recently shown to be in strong linkage disequilibrium (LD) with the CD-associated single nucleotide polymorphisms and is itself associated with CD (P < 0.01). The deletion was correlated with increased or reduced expression of IRGM in transformed cells in a cell line-dependent manner, and has been proposed as a likely causal variant. We report here that small insertion/deletion polymorphisms in the promoter and 5' untranslated region of IRGM are, together with the CNV, strongly associated with CD (P = 1.37 x 10(-5) to 1.40 x 10(-9)), and that the CNV and the 5'-untranslated region variant -308(GTTT)(5) contribute independently to CD susceptibility (P = 2.6 x 10(-7) and P = 2 x 10(-5), respectively). We also show that the CD risk haplotype is associated with a significant decrease in IRGM expression (P < 10(-12)) in untransformed lymphocytes from CD patients. Further analysis of these variants in a Japanese CD case-control sample and of IRGM expression in HapMap populations revealed that neither the IRGM insertion/deletion polymorphisms nor the CNV was associated with CD or with altered IRGM expression in the Asian population. This suggests that the involvement of the IRGM risk haplotype in the pathogenesis of CD requires gene-gene or gene-environment interactions which are absent in Asian populations, or that none of the variants analysed are causal, and that the true causal variants arose after the European-Asian split.
Identifiers		DOI: 10.1093/hmg/ddq041 PMID: 20106866
Full text		Article - Limited access to UNIGE Other version: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2850616/pdf/ddq041.pdf
Structures		Faculté de médecine / Section de médecine clinique / Département de médecine interne des spécialités
Research group		Population Genomics and Genetics of Complex Traits (892)
Citation (ISO format)		PRESCOTT, N. J. et al. Independent and population-specific association of risk variants at the IRGM locus with Crohn's disease. In: Human Molecular Genetics, 2010, vol. 19, n° 9, p. 1828-1839. https://archive-ouverte.unige.ch/unige:8971