Table 5.
Association of nevirapine-induced SJS/TEN and imputed SNPs of the HLA-C locus from the main cohort and the targeted sequencing cohort
| SNP | bp (GRCh37.p13) | A1/A2 | Amino acid substitution | GWAS (discovery cohort) |
Targeted sequencing cohort |
||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| typed/imputed | SJS/TEN MAF (n=51) | control MAF (n=182) | P | OR (95% CI) | SJS/TEN MAF (n = 16) | control MAF (n = 16) | P | OR (95% CI) | LD with rs5010528 (D′) | ||||
| rs146911342 | 31 237 779 | C/T | p.V327M | imputed | 0.36 | 0.15 | 4.13 × 10−6 | 4.75 (2.45–9.23) | 0.34 | 0.13 | 0.013 | 34.14 (2.07–561.6) | 1 |
| rs41562714 | 31 238 538 | G/C | imputed | 0.36 | 0.15 | 4.13 × 10−6 | 4.75 (2.45–9.23) | 0.34 | 0.13 | 0.013 | 34.14 (2.07–561.6) | 1 | |
| rs1050409 | 31 239 501 | G/T | p.A73E | imputed | 0.36 | 0.15 | 4.13 × 10−6 | 4.75 (2.45–9.23) | 0.34 | 0.13 | 0.013 | 34.14 (2.07–561.6) | 1 |
| rs41553018 | 31 239 742 | G/C | imputed | 0.36 | 0.15 | 3.71 × 10−6 | 4.75 (2.45–9.23) | 0.34 | 0.13 | 0.013 | 34.14 (2.07–561.6) | 1 | |
| rs4361609 | 31 240 635 | G/C | imputed | 0.36 | 0.15 | 4.13 × 10−6 | 4.75 (2.45–9.23) | 0.34 | 0.13 | 0.013 | 34.14 (2.07–561.6) | 1 | |
| rs5010528 | 31 241 032 | A/G | typed | 0.36 | 0.15 | 4.13 × 10−6 | 4.75 (2.45–9.23) | 0.34 | 0.13 | 0.013 | 34.14 (2.07–561.6) | – | |
| rs58019823 | 31 241 215 | A/G | imputed | 0.36 | 0.15 | 4.13 × 10−6 | 4.75 (2.45–9.23) | – | – | – | – | NA | |
| ars2524087 | 31241 294 | C/G | imputed | 0.37 | 0.15 | 3.71 × 10−6 | 4.73 (2.45–9.14) | – | – | – | – | NA | |
| ars59103503 | 31 287 944 | G/T | imputed | 0.37 | 0.15 | 2.75 × 10−6 | 5.00 (2.55–9.80) | – | – | – | – | NA | |
| ars77641320 | 31 298 229 | C/G | imputed | 0.35 | 0.14 | 1.64 × 10−6 | 5.53 (2.75–11.12) | – | – | – | – | NA | |
| ars9468965 | 31 300 247 | T/A | imputed | 0.44 | 0.19 | 2.24 × 10−6 | 4.61 (2.24–8.69) | – | – | – | – | NA | |
| ars35364987 | 31 309 423 | T/C | imputed | 0.49 | 0.27 | 8.01 × 10−6 | 3.76 (2.10–6.74) | – | – | – | – | NA | |
| ars35435945 | 31 311 374 | T/G | imputed | 0.49 | 0.27 | 9.83 × 10−6 | 3.72 (2.08–6.67) | – | – | – | – | NA | |
| ars35278939 | 31 319 780 | G/A | imputed | 0.47 | 0.23 | 8.01 × 10−6 | 4.04 (2.19–7.47) | – | – | – | – | NA | |
The list comprises all SNPs with a P value of <1 × 10 − 5 in the main cohort analysis. Statistical significance and OR (95% CI) for the targeted sequencing cohort is determined by logistic regression with CD4+ cell count as covariate. NA denotes LD indeterminable in targeted sequencing cohort as SNP typing not available.
a
SNP was imputed in the discovery cohort analysis but not detected and or called in the sequencing data.