Chunk #26 — Imputation of classical HLA alleles

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The UK Biobank resource with deep phenotyping and genomic data.

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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 × 10−600Homozygote correction0.67 (0.52–0.87)2.32 × 10−30.54 (0.47–0.61)8.50 × 10−22 HLA-A*02:01 Additive effect0.69 (0.62–0.78)2.30 × 10−100.67 (0.64–0.70)7.80 × 10−70Homozygote correction1.20 (0.89–1.62)2.41 × 10−11.26 (1.13–1.41)3.30 × 10−05 HLA-DRB1*03:01 Additive effect1.21 (1.06–1.37)3.39 × 10−31.16 (1.10–1.22)3.50 × 10−08Homozygote correction2.12 (1.53–2.94)6.84 × 10−62.58 (2.19–3.03)1.30 × 10−30 HLA-DRB1*13:03 Additive effect2.10 (1.54–2.85)2.36 × 10−62.62 (2.32–2.96)6.20 × 10−55 HLA-DRB1*08:01 Additive effect1.56 (1.21–2.01)6.13 × 10−41.55 (1.42–1.69)1.00 × 10−23 HLA-B*44:02 Additive effect0.86 (0.74–0.98)2.94 × 10−20.78 (0.74–0.83)4.70 × 10−17 HLA-B*38:01 Additive effect0.29 (0.13–0.65)2.55 × 10−30.48 (0.42–0.56)8.00 × 10−23 HLA-B*55:01 Additive effect0.99 (0.75–1.31)9.47 × 10−10.63 (0.55–0.73)6.90 × 10−11 HLA-DQA1*01:01 Additive effect in the presence of HLA-DRB1*15:010.71 (0.56–0.90)5.33 × 10−30.65 (0.59–0.72)1.30 × 10−17 HLA-DQB1*03:02 Dominant effect1.07 (0.92–1.25)3.71 × 10−11.30 (1.23–1.37)1.80 × 10−22 HLA-DQB1*03:01 Allelic interaction with HLA-DQB1*03:020.8 (0.53–1.20)2.81 × 10−10.60 (0.52–0.69)7.10 × 10−12Evidence for association between HLA alleles and MS in UK Biobank compared to the IMSGC cohort. The UK Biobank association tests involved 1,501 self-reported cases and 409,724 controls; the IMSGC cohort involved 17,465 cases and 30,385 controls31. Thus, the UK Biobank