Table 1.
Step | Position | Alleles* | Position P† | Model P‡ | Cumulative variance explained§ |
1 | HLA-B 97 | V/N/W/T/R/S | 4.6 x 10−143 | na | 0.102 |
2 | HLA-B 67 | Y/F/S/C/M | 3.7 x 10−112 | 3.2 x 10−15 | 0.112 |
3 | HLA-B 45 | E/T/K/M | 8.2 x 10−49 | 1.8 x 10−4 | 0.114 |
4 | HLA-A 77 | N/S/D | 1.8 x 10−12 | 9.4 x 10−12 | 0.122 |
5 | HLA-A 95 | L/I/V | 3.6 x 10−5 | 3.2 x 10−7 | 0.123 |
na, not applicable.
Per allele association statistics and frequencies are listed in SI Appendix, Table S4.
Position P values were calculated by a multi–degree-of-freedom omnibus test, including covariates and all alleles at that position.
Model P values were calculated by the likelihood ratio test comparing the model from the previous step to a model including the next position.
Cumulative variance explained was calculated by linear regression and represents the variance explained by including the positions identified at each step to the model from the previous step.