Institutional members access full text with Ovid®

Share this article on:

Transmission Distortion in Crohn's Disease Risk GeneATG16L1Leads to Sex Difference in Disease Association

Liu, Linda Y. B.S.1,2,3; Schaub, Marc A. M.S.4; Sirota, Marina Ph.D.1,2,3; Butte, Atul J. M.D., Ph.D.1,2,3*

doi: 10.1002/ibd.21781
Original Article: Original Basic Science Articles

Background: Crohn's disease (CD), an inflammatory disease of the bowel, affects millions of people around the world. Evidence suggests that disease onset and pathogenesis differ between males and females. Yet no comprehensive efforts exist to assess the sex-specific genetic architecture of CD.

Methods: We used genotyping data from a cohort of 1748 CD cases and 2938 controls to investigate 71 meta-analysis-confirmed CD risk loci for sex differences in disease risk. We further validated the significant results in separate cohorts of 968 CD cases and 2809 controls, and performed a meta-analysis across datasets.

Results: The single nucleotide polymorphism (SNP) rs3792106 (C/T) in ATG16L1 showed a significant sex effect with P-value 6.9 × 10−13 and allelic odds ratio 1.48 in females, and P-value 0.013 and odds ratio 1.22 in males (odds ratio heterogeneity P-value 0.037). Surprisingly, the difference was found to arise from a discrepancy in allele frequencies between male and female controls (P-value 0.0045) rather than cases. We found similar results for this SNP in the separate validation datasets. Using 155 HapMap 3 trios, we detected significant maternal overtransmission of the T allele at rs3792106 (P-value 0.027).

Conclusions: Our results indicate that different transmission patterns between sexes may sustain the disparate allele frequencies at rs3792106 in healthy populations, and furthermore that a virus-risk variant mechanism implicated in CD alters the distribution in diseased patients. To our knowledge, this is the first report of sex-specific CD association in ATG16L1. The possible implications in CD and basic human biology present interesting areas for future investigation. (Inflamm Bowel Dis 2011;)

1Stanford Center for Biomedical Informatics Research, Stanford University School of Medicine, Stanford, California

2Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, California

3Lucile Packard Children's Hospital, Palo Alto, California

4Computer Science Department, Stanford University, Stanford, California

*Stanford University School of Medicine, 251 Campus Dr., MS-5415, Room X-163, Stanford, CA 94305-5415


Received 14 April 2011; Accepted 25 April 2011

Published online 25 May 2011 in Wiley Online Library (

Grant sponsor: Hewlett family Stanford Graduate Fellowship; Grant sponsor: National Science Foundation Graduate Research Fellowship; Grant sponsor: Richard and Naomi Horowitz Stanford Graduate Fellowship; Grant sponsor: US National Library of Medicine; Grant Number: T15 LM007033; Grant sponsor: US National Institute of General Medical Sciences; Grant Number: R01 GM079719.

Additional Supporting Information may be found in the online version of this article.

© Crohn's & Colitis Foundation of America, Inc.
You currently do not have access to this article

To access this article:

Note: If your society membership provides full-access, you may need to login on your society website