Table 2. AUC and MCC from functional inference tools for PharmGKB category 1 (Type A enriched) vs PharmGKB category 3 and 4 (Type B enriched) pharmacogenetic variants.
| Algorithm | Type A or Type B enriched | Area under curve (AUC) | Matthews correlation coefficient (MCC) |
|---|---|---|---|
| PolyPhen2 | Type A | 0.852 | 0.489 |
| MutPred | Type A | 0.975 | 0.788 |
| REVEL | Type A | 0.942 | 0.794 |
| SIFT | Type A | 0.774 | 0.358 |
| CADD | Type A | 0.728 | 0.321 |
| Mutation assessor | Type A | 0.763 | 0.396 |
| PolyPhen2 | Type B | 0.397 | 0.00338 |
| MutPred | Type B | 0.682 | 0.300 |
| REVEL | Type B | 0.498 | 0.106 |
| SIFT | Type B | 0.410 | −0.0400 |
| CADD | Type B | 0.461 | 0.118 |
| Mutation assessor | Type B | 0.427 | 0.0764 |
| Average Type A | 0.839 | 0.524 | |
| Average Type B | 0.479 | 0.094 |