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Genome-wide association study identifies new susceptibility loci for Crohn disease and implicates autophagy in disease pathogenesis


We present a genome-wide association study of ileal Crohn disease and two independent replication studies that identify several new regions of association to Crohn disease. Specifically, in addition to the previously established CARD15 and IL23R associations, we identified strong and significantly replicated associations (combined P < 10−10) with an intergenic region on 10q21.1 and a coding variant in ATG16L1, the latter of which was also recently reported by another group. We also report strong associations with independent replication to variation in the genomic regions encoding PHOX2B, NCF4 and a predicted gene on 16q24.1 (FAM92B). Finally, we demonstrate that ATG16L1 is expressed in intestinal epithelial cell lines and that functional knockdown of this gene abrogates autophagy of Salmonella typhimurium. Together, these findings suggest that autophagy and host cell responses to intracellular microbes are involved in the pathogenesis of Crohn disease.

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Figure 1: Genome-wide association results for 946 ileal Crohn disease cases and 977 control samples.
Figure 2: Expression of autophagy components in human cell lines and primary immune cells.
Figure 3: ATG16L1 is required for autophagy of Salmonella typhimurium.


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We thank the patients and their families for participating in these studies. We are grateful to all of the clinicians, research nurses and study coordinators for their contributions to the work. We thank D. Caplan, G. Charron, C. Labbé, C. Lefebvre and D. Miclaus for their help in the preparation of the manuscript; J. Adams for help with immunohistochemistry; A. Landry for expression studies and D. Altshuler for his critical reading of the manuscript. The NIDDK IBDGC is funded by the following grants: DK62431 (S.R.B.), DK62420 (R.H.D.), DK62432 (J.D.R.), DK62423 (M.S.S.), DK62413 (K.D.T.) and DK62422 and DK62429 (J.H.C.). The work on the Cedars-Sinai cohort was supported by project 1 of DK 46763 (J.I.R.). R.J.X. is supported by the following grants: AI062773 and DK43351.

Author information

Authors and Affiliations



S.R.B., J.H.C., R.H.D., E.-J. B., M.R., J.D.R., J.I.R., M.S., A.H.S., L.W.D, Y.Y.S. and K.D.T. collected patient samples and clinical information. S.R.B., J.H.C., M.J.D., R.H.D., J.D.R. and M.S. designed the genome-wide study. J.H.C., M.J.D., P.G., J.D.R., J.I.R., S.R.B. and K.D.T. designed the replication study. T.G. and P.G. analyzed the genome-wide and replication data, respectively, with contributions from M.M.B. and D.N., under the supervision of M.J.D. and J.D.R. L.M. analyzed the Cedars-Sinai ATG16L1 genetic data under the supervision of K.D.T. and J.I.R. P.K. and A.H. performed molecular and cellular biology experiments, under the supervision of R.J.X. The manuscript was written by M.J.D., J.D.R. and R.J.X., with contributions from S.R.B., J.H.C., R.H.D., M.S., A.H., P.G., A.H.S., Y.Y.S., D.L.N. and K.D.T. J.D.R. coordinated the analysis and manuscript writing efforts of this multicenter study.

Corresponding author

Correspondence to John D Rioux.

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Competing interests

A.H.S. is on the Scientific Advisory Boards of Shire Pharmaceuticals, Schering (Canada) and Procter & Gamble Pharmaceuticals.

R.H.D. has received honoraria for speaking in Illumina's educational seminar series about research projects that have used Illumina's products.

Supplementary information

Supplementary Fig. 1

Association and linkage disequilibrium patterns surrounding the ATG16L1, PHOX2B, 10q, NCF4 and FAM92B novel loci. (PDF 483 kb)

Supplementary Fig. 2

Conservation of the threonine allele at position 197 of the ATG16L1 gene. (PDF 18 kb)

Supplementary Fig. 3

PHOX2B expression is confined to a subset of gut cells in both mouse and human tissues. (PDF 2439 kb)

Supplementary Fig. 4

Expression pattern of NCF4 in primary immune cells. (PDF 10 kb)

Supplementary Fig. 5

Knockdown of ATG16L1 prevents induction of autophagy by classical stimuli. (PDF 347 kb)

Supplementary Fig. 6

Quality control assessment of the GWA data. (PDF 111 kb)

Supplementary Table 1

Phenotypic subgroup analysis of confirmed loci. (PDF 38 kb)

Supplementary Table 2

Primer sequences for real-time RT-PCR assays for RNA quantitation experiments. (PDF 14 kb)

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Rioux, J., Xavier, R., Taylor, K. et al. Genome-wide association study identifies new susceptibility loci for Crohn disease and implicates autophagy in disease pathogenesis. Nat Genet 39, 596–604 (2007).

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