Table 2.
Summary of genotypes for 10 ADME genes inferred by Aldy on GeT-RM samples (137 PGRNseq v.1 samples) and Coriell samples (17 PGRNseq v.2 samples)
| PGRNseq v.1 | Matches | Improvements | Mismatches | Unknown | Total |
|---|---|---|---|---|---|
| CYP2A6 | 110 | 18 | 3 | 6 | 137 |
| CYP2C8 | 137 | 0 | 0 | 0 | 137 |
| CYP2C9 | 136 | 1 | 0 | 0 | 137 |
| CYP2C19 | 128 | 9 | 0 | 0 | 137 |
| CYP2D6 | 107 | 27 | 0 | 3 | 137 |
| CYP3A4 | 131 | 6 | 0 | 0 | 137 |
| CYP3A5 | 137 | 0 | 0 | 0 | 137 |
| CYP4F2 | 121 | 16 | 0 | 0 | 137 |
| DPYD | 79 | 56 | 0 | 2 | 137 |
| TPMT | 135 | 2 | 0 | 0 | 137 |
| Total | 1221 | 135 | 3 | 11 | 1370 |
| 89% | 10% | 0.2% | 0.8% | 100% | |
| PGRNseq v.2 | Matches | Improvements | Mismatches | Unknown | Total |
| CYP2A6 | 14 | 2 | 0 | 1 | 17 |
| CYP2C8 | 17 | 0 | 0 | 0 | 17 |
| CYP2C9 | 17 | 0 | 0 | 0 | 17 |
| CYP2C19 | 16 | 1 | 0 | 0 | 17 |
| CYP2D6 | 87 | 9 | 0 | 0 | 96 |
| CYP3A4 | 17 | 0 | 0 | 0 | 17 |
| CYP3A5 | 17 | 0 | 0 | 0 | 17 |
| CYP4F2 | 15 | 2 | 0 | 0 | 17 |
| DPYD | 9 | 8 | 0 | 0 | 17 |
| TPMT | 17 | 0 | 0 | 0 | 17 |
| Total | 226 | 22 | 0 | 1 | 249 |
| 91% | 8.6% | 0% | 0.4% | 100% |
“Matches” column indicates the concordance between Aldy’s call and panel prediction, while “Mismatches” indicates the discordance. “Improvements” column indicates the potential improvement of Aldy’s calls over the genotyping panels. Finally, “Unknown” indicates the samples for which further validation is needed to clearly call the correct genotype. Further details are available in the Supplementary Discussion