Investigating the genetic association between ERAP1 and ankylosing spondylitis

Abstract

A strong association between ERAP1 and ankylosing spondylitis (AS) was recently identified by the Wellcome Trust Case Control Consortium and the Australo-Anglo-American Spondylitis Consortium (WTCCC-TASC) study. ERAP1 is highly polymorphic with strong linkage disequilibrium evident across the gene. We therefore conducted a series of experiments to try to identify the primary genetic association(s) with ERAP1. We replicated the original associations in an independent set of 730 patients and 1021 controls, resequenced ERAP1 to define the full extent of coding polymorphisms and tested all variants in additional association studies. The genetic association with ERAP1 was independently confirmed; the strongest association was with rs30187 in the replication set (P = 3.4 x 10(-3)). When the data were combined with the original WTCCC-TASC study the strongest association was with rs27044 (P = 1.1 x 10(-9)). We identified 33 sequence polymorphisms in ERAP1, including three novel and eight known non-synonymous polymorphisms. We report several new associations between AS and polymorphisms distributed across ERAP1 from the extended case-control study, the most significant of which was with rs27434 (P = 4.7 x 10(-7)). Regression analysis failed to identify a primary association clearly; we therefore used data from HapMap to impute genotypes for an additional 205 non-coding SNPs located within and adjacent to ERAP1. A number of highly significant associations (P < 5 x 10(-9)) were identified in regulatory sequences which are good candidates for causing susceptibility to AS, possibly by regulating ERAP1 expression.

Figure 1.

SNP association with AS against genomic location. Log₁₀ P-value for imputed and genotyped SNPs plotted against physical distance. Aligned to the plot are the genomic location of two ERAP1 isoforms and LD that exists in this region, red regions indicating high LD and blue indicating low LD.

Figure 2.

Comparison of the strength of association of various ERAP1 SNPs with AS and their influence on ERAP1 expression. P-values for association of SNPs with AS generated by genotyping or imputation in our extended cases–control study were compared with P-values for SNP association with ERAP1 transcript abundance from a previous study (using data from probe 209788_s_at) (18). Only a subset of 32 SNPs are plotted which were used in both studies.

Figure 3.

Ribbon model of putative ERAP1 structure. Highlighted are the active site around the central Zn atom (red sphere) in cyan and the positions of residues affected by non-synonymous polymorphisms associated with AS in this study, including rare novel variants V647I and C736R.