Amino acid position 11 of HLA-DRβ1 is a major determinant of chromosome 6p association with ulcerative colitis

Abstract

The major histocompatibility complex (MHC) on chromosome 6p is an established risk locus for ulcerative colitis (UC) and Crohn's disease (CD). We aimed to better define MHC association signals in UC and CD by combining data from dense single-nucleotide polymorphism (SNP) genotyping and from imputation of classical human leukocyte antigen (HLA) types, their constituent SNPs and corresponding amino acids in 562 UC, 611 CD and 1428 control subjects. Univariate and multivariate association analyses were performed, controlling for ancestry. In univariate analyses, absence of the rs9269955 C allele was strongly associated with risk for UC (P = 2.67 × 10(-13)). rs9269955 is a SNP in the codon for amino acid position 11 of HLA-DRβ1, located in the P6 pocket of the HLA-DR antigen binding cleft. This amino acid position was also the most significantly UC-associated amino acid in omnibus tests (P = 2.68 × 10(-13)). Multivariate modeling identified rs9269955-C and 13 other variants in best predicting UC vs control status. In contrast, there was only suggestive association evidence between the MHC and CD. Taken together, these data demonstrate that variation at HLA-DRβ1, amino acid 11 in the P6 pocket of the HLA-DR complex antigen binding cleft is a major determinant of chromosome 6p association with UC.

Figure 1

Major histocompatibility complex regional association plots for ulcerative colitis. (A) Association results for genotyped SNPs from the Illumina Omni1-quad BeadChip. The intensity of the red shading indicates the strength of the pairwise r² correlation to the most associated SNP, rs2647025. (B) Association results for both genotyped (◇ symbols) and imputed (■ symbols) nucleotides focused in on the region of peak association in panel A. Horizontal lines represent the classical HLA alleles in this region. The intensity of the red shading indicates the strength of the pairwise r² correlation to the most associated SNP marker, rs9269955-C. (C) Association results for imputed amino acids in HLA-DRβ1.

Figure 2

Major histocompatibility complex regional association plot for Crohn’s disease with ileal involvement. Association results are for genotyped SNPs from the Illumina Omni1-quad BeadChip. The intensity of the red shading indicates the strength of the pairwise r² correlation to the most associated SNP, rs17880124.