To demonstrate the utility of the HLA imputation, we performed association tests for diseases known to have HLA associations. We analysed 409,724 individuals in the white British ancestry subset (see Methods) and focused on 11 self-reported immune-mediated diseases with known HLA associations. For each disease in our analysis, we identified the HLA allele with the strongest evidence of association. In all cases these were consistent with previous reports (see Methods and Supplementary Table 9). We further replicated independent HLA associations in a single disease study of multiple sclerosis (MS) susceptibility by the International Multiple Sclerosis Genetics Consortium (IMSGC)31. Here we observed evidence of association and effect size estimates for HLA alleles that are concordant in direction and relative magnitude with those found in the IMSGC study, although in 11 out of 14 cases this was closer to 1, consistent with regression dilution bias arising from a low rate of phenotypic error (Table 1).Table 1Association between HLA alleles and MS in UK Biobank and IMSGC cohortHLA alleleTestUK BiobankIMSGCOR (95% CI)P valueOR (95% CI)P value HLA-DRB1*15:01 Additive effect3.16 (2.81–3.54)2.58 × 10−853.92 (3.74–4.12)<1
