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Pathway-based Genome-wide Association Studies Reveal the Association Between Growth Factor Activity and Inflammatory Bowel Disease

Li, Jin PhD; Wei, Zhi PhD; Chang, Xiao PhD; Cardinale, Christopher J. MD, PhD; Kim, Cecilia E. BA; Baldassano, Robert N. MD; Hakonarson, Hakon MD, PhDand the International IBD Genetics Consortium

doi: 10.1097/MIB.0000000000000785
Original Basic Science Articles

Background: The inflammatory bowel diseases known as Crohn's disease (CD) and ulcerative colitis (UC) are related autoimmune conditions with a complex etiology composed of genetic and environmental factors. Genetic studies have revealed 200 susceptibility loci for inflammatory bowel diseases, but these only account for a small fraction of the genetic heritability of the disease. We employed pathway-based approaches to identify genes that cooperatively make contributions to the genetic etiology of CD.

Methods: We exploited the largest CD dataset (20,000 cases + 28,000 controls) and UC dataset (17,000 cases + 33,500 controls) to date. We conducted a meta-analysis of 5 CD cohorts of European ancestry using 3 pathway-based approaches and further performed replication studies in an independent cohort genotyped on the Immunochip and in another pediatric cohort of European ancestry. Similar meta-analysis was performed for UC cohorts.

Results: In addition to the multiple immune-related pathways that have been implicated in the genetic etiology of inflammatory bowel diseases before, we found significant associations involving genes in growth factor signaling for CD. This result was replicated in 2 independent cohorts of European ancestry. This association with growth factor activity is not unique to CD. We found a similar significant association with UC cohorts.

Conclusions: Our findings suggest that genes involved in pathways of growth factor signaling may make joint contributions to the etiology of CD and UC, providing novel insight into the genetic mechanisms of these diseases.

Supplemental Digital Content is Available in the Text.Article first published online 22 April 2016.

*Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania;

Department of Computer Science, New Jersey Institute of Technology, Newark, New Jersey;

Center for Pediatric Inflammatory Bowel Disease, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania;

§Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania; and

Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.

Reprints: Zhi Wei, PhD, Department of Computer Science, College of Computing Sciences, New Jersey Institute of Technology, GITC 4400, University Heights, Newark, NJ 07102 (e-mail:

Supplemental digital content is available for this article. Direct URL citations appear in the printed text and are provided in the HTML and PDF versions of this article on the journal's Web site (

Supported by an Institutional Development Fund from the Children's Hospital of Philadelphia and an Adele S. and Daniel S. Kubert Estate gift to the Center for Applied Genomics.

The authors have no conflict of interest to disclose. A full list of members of the International IBD Genetics Consortium can be found in the Supplementary Information.

Received January 15, 2016

Accepted February 25, 2016

© Crohn's & Colitis Foundation of America, Inc.
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