Table 3. The comparison of four-digit accuracies for HIBAG and HLA*IMP on HLARES data of European ancestry with no call threshold.
|
HLA type |
|||||
|---|---|---|---|---|---|
| Method | A | B | C | DRB1 | DQB1 |
| No.of validation samples | 1787 | 2471 | 1830 | 2383 | 1917 |
| Using 191 markers on Illumina 1M platform as selected by HLA*IMPa | |||||
| No.of SNPs | 50 | 39 | 27 | 50 | 34 |
| HLA*IMP (%) | 91.0 | 94.4 | 98.4 | 87.9 | 96.2 |
| HIBAG b (%) | 96.7 | 94.8 | 98.7 | 90.0 | 98.6 |
| Using all the xMHC markers on Illumina 1M platformc | |||||
| No. of SNPs | 489 | 562 | 554 | 474 | 447 |
| HIBAGb (%) | 97.7 | 95.1 | 98.7 | 91.8 | 98.4 |
Abbreviations: HLA, human leukocyte antigen; MHC, major histocompatibility complex; SNP, single-nucleotide polymorphism.
a
The full SNP list is shown in Supplementary Table S4.
b
The training samples are HapMap 30 CEU trios plus WTCCC samples.
c
The SNP markers within a flanking region of 250 kb are used.