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


We performed a genome-wide association study of 19,779 nonsynonymous SNPs in 735 individuals with Crohn disease and 368 controls. A total of 7,159 of these SNPs were informative. We followed up on all 72 SNPs with P ≤ 0.01 with an allele-based disease association test in 380 independent Crohn disease trios, 498 Crohn disease singleton cases and 1,032 controls. Disease association of rs2241880 in the autophagy-related 16-like 1 gene (ATG16L1) was replicated in these samples (P = 4.0 × 10−8) and confirmed in a UK case-control sample (P = 0.0004). By haplotype and regression analysis, we found that marker rs2241880, a coding SNP (T300A), carries virtually all the disease risk exerted by the ATG16L1 locus. The ATG16L1 gene encodes a protein in the autophagosome pathway that processes intracellular bacteria. We found a statistically significant interaction with respect to Crohn disease risk between rs2241880 and the established CARD15 susceptibility variants (P = 0.039). Together with the lack of association between rs2241880 and ulcerative colitis (P > 0.4), these data suggest that the underlying biological process may be specific to Crohn disease.

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Figure 1: Expression and cellular localization of the ATG16L1 gene product.
Figure 2: Three-dimensional structural model of the WD-repeat domain of human ATG16L1.

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We thank all affected individuals, families and physicians for their cooperation. We acknowledge the cooperation of the German Crohn and Colitis Patient Association (Deutsche Morbus Crohn und Colitis Vereinigung) and the contributing gastroenterologists. The authors thank T. Wesse, B. Petersen, L. Bossen, T. Henke, S. Ehlers, A. Dietsch, T. Kaacksteen and D. Soars for technical help. The ongoing technical and logistic support and helpful discussions with A. Toeppel, C.R. Scafe, A. Kejariwal, H.M. Wenz, M. Rhodes, S. Short, T. Woodage and D.A. Gilbert from Applied Biosystems is especially acknowledged. We thank C.-C. Chiang for preparing the submission of new SNPs to dbSNP. T.H. Karlsen (Rikshospitalet) is acknowledged for helpful discussions. We thank A. Forbes, J. Sanderson and S. Fisher for case ascertainment and establishment of the UK Crohn disease database. We acknowledge use of genotype data from the British 1958 Birth Cohort DNA collection, funded by Medical Research Council grant G0000934 and Wellcome Trust grant 068545/Z/02. This study was supported by the German Ministry of Education and Research (BMBF) through the National Genome Research Network (environmental diseases network and SMP-GEM), the POPGEN biobank, the analysis infrastructure and methods of the MediGrid project and the German Research Council (Ha 3091/1-1, 2-1), Applied Biosystems, TECAN, the Wellcome Trust and CORE (UK).

Author information




J.H. and A.F. established the genotyping and analysis methodology; A.F. performed the genotyping and association analysis and contributed to the writing of the manuscript; S.S. supervised the patient recruitment; J.H. recruited the German patients and drafted the manuscript; P.R., A.T., A.F., K.H., R.H., B.S. and M.P. performed the protein, immunohistochemistry and cDNA experiments; M.T. provided LIMS programming support; M.A., G.M. and T.L. performed in silico protein analysis and contributed to writing the manuscript; F.D.L.V. designed the cSNP panel and genotyping assays and contributed to the manuscript; J.B. and S.G. helped establish the SNPlex automation system; N.P., C.O. and C.M. performed the replication experiment in the UK samples; U.F. contributed to the design and the writing of the paper; M.K. provided genetic epidemiology consulting, performed the interaction analysis and helped draft the manuscript; and J.H. and S.S. jointly designed and supervised the experiment.

Corresponding authors

Correspondence to Jochen Hampe or Stefan Schreiber.

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Competing interests

A patent application has been filed regarding ATG16L1 as a susceptibility gene for Crohn disease.

Supplementary information

Supplementary Fig. 1

Overview of the physical and genetic structure of the ATG16L1 region. (PDF 118 kb)

Supplementary Table 1

Full list of the top 72 SNPs fulfilling follow-up criteria. (PDF 24 kb)

Supplementary Table 2

Frequencies of rs2241880 genotypes in different subphenotype groups of the German cases. (PDF 9 kb)

Supplementary Table 3

Fine mapping of the CD association signal at the ATG16L1 locus. (PDF 13 kb)

Supplementary Table 4

Comprehensive list of nonsynonymous SNPs, with design details. (PDF 3105 kb)

Supplementary Table 5

Primer sequences used for mutation detection of ATG16L1. (PDF 13 kb)

Supplementary Table 6

Primer sequences used for RT-PCR amplification of the ATG16L1 transcript. (PDF 11 kb)

Supplementary Methods (PDF 147 kb)

Supplementary Note (PDF 317 kb)

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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 39, 207–211 (2007).

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