Table 4.
Imputation accuracy without any processing, then with the filtering applied with our scoring method
| Gene | Test population | Base imputation | People removed | Sub-population imputation |
|---|---|---|---|---|
| HLA (two-field) | ||||
| HLA-A | 865 | 97.6 | 30 (40% correct) | 99.6 |
| HLA-B | 1495 | 96 | 112 (65% correct) | 98.5 |
| HLA-C | 813 | 95.8 | 81 (60% correct) | 99.5 |
| HLA-DQB1 | 974 | 94.8 | 40 (60% correct) | 96.1 |
| HLA (one-field) | ||||
| HLA-A | 1669 | 97.8 | 62 (40% correct) | 99.9 |
| HLA-B | 1562 | 97.1 | 119 (70% correct) | 99.5 |
| HLA-C | 1291 | 95.8 | 125 (60% correct) | 99.9 |
| HLA-DQB1 | 1701 | 98.2 | 175 (90% correct) | 99.2 |
T1DGC was used as our reference panel and 1958BC as our test panel. We also precise the percentage of correct imputations that were removed