Deep Resequencing of GWAS Loci Identifies Rare Variants in CARD9, IL23R and RNF186 That Are Associated with Ulcerative Colitis

Mélissa Beaudoin,Rinse K Weersma,Ken Sin Lo,John D Rioux,David Ellinghaus,Ramnik J Xavier,Caroline Lagacé,Jonas Halfvarson,Stefan Schreiber,Guillaume Lettre,Alain Bitton,Philippe Goyette,Richard H Duerr,Francesca Bresso,Manuel A Rivas,Mark S Silverberg,Azadeh Alikashani,Leif Törkvist,Christine Stevens,Mark J Daly,Judy H Cho,Gautam Goel,Jakob Begun,Martin Ladouceur,Gabrielle Boucher,Vito Annese,Yashoda Sharma,Graham Radford‐Smith ,Dermot P Mcgovern ,L Philip Schumm ,Mauro D’amato ,Séverine Vermeire ,Steve Brant ,André Franke

doi:10.1371/journal.pgen.1003723

Abstract

Genome-wide association studies and follow-up meta-analyses in Crohn's disease (CD) and ulcerative colitis (UC) have recently identified 163 disease-associated loci that meet genome-wide significance for these two inflammatory bowel diseases (IBD). These discoveries have already had a tremendous impact on our understanding of the genetic architecture of these diseases and have directed functional studies that have revealed some of the biological functions that are important to IBD (e.g. autophagy). Nonetheless, these loci can only explain a small proportion of disease variance (∼14% in CD and 7.5% in UC), suggesting that not only are additional loci to be found but that the known loci may contain high effect rare risk variants that have gone undetected by GWAS. To test this, we have used a targeted sequencing approach in 200 UC cases and 150 healthy controls (HC), all of French Canadian descent, to study 55 genes in regions associated with UC. We performed follow-up genotyping of 42 rare non-synonymous variants in independent case-control cohorts (totaling 14,435 UC cases and 20,204 HC). Our results confirmed significant association to rare non-synonymous coding variants in both IL23R and CARD9, previously identified from sequencing of CD loci, as well as identified a novel association in RNF186. With the exception of CARD9 (OR = 0.39), the rare non-synonymous variants identified were of moderate effect (OR = 1.49 for RNF186 and OR = 0.79 for IL23R). RNF186 encodes a protein with a RING domain having predicted E3 ubiquitin-protein ligase activity and two transmembrane domains. Importantly, the disease-coding variant is located in the ubiquitin ligase domain. Finally, our results suggest that rare variants in genes identified by genome-wide association in UC are unlikely to contribute significantly to the overall variance for the disease. Rather, these are expected to help focus functional studies of the corresponding disease loci.

Highlights

Inflammatory bowel diseases (IBDs) are classified as chronic relapsing inflammatory diseases of the gastrointestinal tract
A prime example of this can be seen with the 163 genetic risk factors that have recently been associated with the chronic inflammatory bowel diseases known as Crohn’s disease and ulcerative colitis
The current study used an approach to directly look at the genetic code for a subset of these and identified a causative change in the genetic code for eight risk factors for ulcerative colitis

Summary

Introduction

Inflammatory bowel diseases (IBDs) are classified as chronic relapsing inflammatory diseases of the gastrointestinal tract. The two major forms of IBDs are Crohn’s disease (CD, OMIM 266600) and ulcerative colitis (UC, OMIM 191390). While some loci were shown to be specific to either CD or UC risk, most have been shown to impact on both diseases, supporting earlier claims that these diseases share genetic risk factors [2]. These recent studies have identified important disease pathways but the common SNPs identified, with generally modest effects, explain only 14% and 7.5% of disease variance for CD and UC, respectively [3]

Methods

Results

Discussion

Conclusion