Table 4. Concordance rate and call rate for important disease-associated and adverse drug reaction-associated alleles.
| HLA Allele | Disease/ADR | Imputation Program | Concordance Rate (EAs)1 | Concordance Rate (AAs)1 |
|---|---|---|---|---|
| B*27:05 | ankylosing spondylitis[24] | SNP2HLA | 0.948 | 0.667 |
| HLA*IMP:02 | 0.936 | 0.250 | ||
| HIBAG | 0.933 | 1.000 | ||
| B*57:01 | abacavir HSN[17]; flucloxacillin DILI[25] | SNP2HLA | 0.996 | 1.000 |
| HLA*IMP:02 | 0.978 | 0.118 | ||
| HIBAG | 0.975 | 1.000 | ||
| B*58:01 | allopurinol SJS/TEN[26] | SNP2HLA | 1.000 | 0.857 |
| HLA*IMP:02 | 1.000 | 0.621 | ||
| HIBAG | 0.964 | 0.783 | ||
| DQB1*02:01 | Sjogren’s Syndrome[27] | SNP2HLA | 0.980 | 0.518 |
| HLA*IMP:02 | 0.997 | 0.957 | ||
| HIBAG | 0.997 | 0.698 | ||
| DRB1*03:02 | Lupus erythematosus[28] | SNP2HLA | 0.750 | 1.000 |
| HLA*IMP:02 | - | - | ||
| HIBAG | 1.000 | 0.951 | ||
| DRB1*08:01 | primary biliary cirrhosis[29] | SNP2HLA | 0.978 | 1.000 |
| HLA*IMP:02 | 0.882 | 0.154 | ||
| HIBAG | 0.951 | - | ||
| DRB1*04:01 | rheumatoid arthritis[30] | SNP2HLA | 0.951 | 0.889 |
| HLA*IMP:02 | 0.856 | 0.179 | ||
| HIBAG | 0.927 | 0.158 |
Concordance rates were generated using HumanOmni1-QUAD and HumanOmni5-QUAD combined SNP-level data and posterior probability>0.50 for each imputation program by HLA locus and race/ethnicity. HLA indicates human leukocyte antigen; EA, European American; AA, African American; HSN, hypersensitivity; DILI, drug-induced liver injury; NA, not applicable; SJS, Stevens-Johnson Syndrome; TEN, toxic epidermal necrosis
1) “-”indicates that the imputation program did not impute the allele.