Genome-wide association study of ulcerative colitis identifies three new susceptibility loci, including the HNF4A region

Abstract

Ulcerative colitis is a common form of inflammatory bowel disease with a complex etiology. As part of the Wellcome Trust Case Control Consortium 2, we performed a genome-wide association scan for ulcerative colitis in 2,361 cases and 5,417 controls. Loci showing evidence of association at P < 1 x 10(-5) were followed up by genotyping in an independent set of 2,321 cases and 4,818 controls. We find genome-wide significant evidence of association at three new loci, each containing at least one biologically relevant candidate gene, on chromosomes 20q13 (HNF4A; P = 3.2 x 10(-17)), 16q22 (CDH1 and CDH3; P = 2.8 x 10(-8)) and 7q31 (LAMB1; P = 3.0 x 10(-8)). Of note, CDH1 has recently been associated with susceptibility to colorectal cancer, an established complication of longstanding ulcerative colitis. The new associations suggest that changes in the integrity of the intestinal epithelial barrier may contribute to the pathogenesis of ulcerative colitis.

Figure 1

−log₁₀(P) values from the 1 d.f. trend test. Alternating chromosomes shown in shades of blue. SNPs with P < 1×10-5 which had not been previously reported are highlighted in green. The three new loci identified in this study are noted.

Figure 2

−log₁₀(P) values from the 1 d.f. trend test from three new loci, along with local recombination rate estimated from HapMap data. Combined P values for replicated SNPs are indicated with a red diamond.