Table 1.
CPIC important genes included a total of 127 CPIC important variants
| Gene | Number of CPIC important variants | Affymetrix DMET and add-on assays |
Whole exome sequencing |
Whole genome sequencing |
|||
|---|---|---|---|---|---|---|---|
| SNV (exonic) | Indel (exonic) | Other | Total | ||||
| CFTR | 10 (1N0) | 2 (2) | 12 | Not interrogated | 12 | 12 | |
| CYP2C19 | 8 (7) | 0 | 8 | 8 | 7 | 8 | |
| CYP2C9 | 10 (10) | 2 (2) | 12 | 10 | 12 | 12 | |
| CYP2D6 | 26 (24) | 13 (13) | 2 structural variations | 41 | 23 and two structural variations | 36 and CYP2D6 copy number (missing CYP2D6/2D7 hybrid) | 35 and CYP2D6 copy number (missing CYP2D6/2D7 hybrid, lower call rate due to copy number variation) |
| CYP3A5 | 2 (1) | 1 (1) | 3 | 3 | 2 (missing important variants) | 3 | |
| DPYD | 10 (10) | 2 (2) | 12 | 9 (missing important variants) | 12 | 12 | |
| G6PD | 7 (7) | 0 | 7 | 4 (missing important variants) | 7 | 2 (lowercall rate due to copy number variation) | |
| HLA-B | 0 | 0 | 1 haplotype | 1 | Not interrogated | 1 | 1 |
| IFNL3 | 2 (0) | 0 | 2 | Not interrogated | Missing important variants | 2 | |
| SLCO1B1 | 12 (11) | 0 | 12 | 10 | 11 | 12 | |
| TPMT | 15 (15) | 0 | 15 | 5 | 15 | 15 | |
| UGT1A1 | 0 | 1 (0) | 1 | Low call rate | 1 | 1 | |
| VKORC1 | 1 (0) | 0 | 1 | 1 | Missing important variants | 1 | |
| Total | 103 (95) | 21 (20) | 3 | 127 | |||
Genotyping performance by DMET, WES, and WGS is summarized as the number of variants interrogated with call rate >98%.