Table 2.
Assay Results: Intra-assay and Interassay Concordance, Accuracy, Precision, Sensitivity, and Specificity
| Gene | rs number | TaqMan assay ID | Intra-assay concordance | Interassay concordance | Verified by Sanger sequencing | Accuracy | Robustness∗ | Analytical sensitivity | Analytical specificity |
|---|---|---|---|---|---|---|---|---|---|
| ABCB1 | rs1045642 | C___7586657_20 | 100% (12 samples in triplicate) | 100% (18 samples in triplicate) | Yes | 100% (12 samples) | Yes | 100% (95% CI, 93–100) | 100% (95% CI, 83–100) |
| rs1128503 | C___7586662_10 | ||||||||
| rs2032582 | C_11711720C_30 | ||||||||
| CBR3 | rs1056892 | C___9483603_10 | 100% (14 samples in triplicate) | 100% (18 samples in triplicate) | Yes | 100% (11 samples) | Yes | 100% (95% CI, 68–100) | 100% (95% CI, 78–100) |
| COMT | rs4646316 | C__29193982_10 | 100% (14 samples in triplicate) | 100% (18 samples in triplicate) | Yes | 100% (11 samples) | Yes | 100% (95% CI, 77–100) | 100% (95% CI, 89–100) |
| rs9332377 | C__29614343_10 | ||||||||
| CYP3A7 | rs45446698 (*1C) | C__30634320_10 | 100% (14 samples in triplicate) | 100% (18 samples in triplicate) | No | 100% (96 samples) | Yes | 100% (95% CI, 51–100) | 100% (95% CI, 98–100) |
| C8orf34 | rs1517114 | C___8341581_20 | 100% (7 samples in triplicate) | 100% (7 samples in triplicate) | Yes | 100% (16 samples) | Yes | 100% (95% CI, 86–100) | 100% (95% CI, 68–100) |
| FCGR2A | rs1801274 | C___9077561_20 | 100% (14 samples in triplicate) | 100% (18 samples in triplicate) | Yes | 100% (9 samples) | Yes | 100% (95% CI, 70–100) | 100% (95% CI, 70–100) |
| FCGR3A | rs396991 | C__25815666_10 | 100% (14 samples in triplicate) | 100% (18 samples in triplicate) | Yes | 100% (10 samples) | Yes | 100% (95% CI, 72–100) | 100% (95% CI, 90–100) |
| HAS3 | rs2232228 | C___3283947_1_ | 100% (14 samples in triplicate) | 100% (18 samples in triplicate) | Yes | 100% (12 samples) | Yes | 100% (95% CI, 68–100) | 100% (95% CI, 81–100) |
| NT5C2 | rs11598702 | C__11196884_20 | 100% (7 samples in triplicate) | 100% (7 samples in triplicate) | Yes | 100% (16 samples) | Yes | 100% (95% CI, 61–100) | 100% (95% CI, 87–100) |
| NUDT15 | rs116855232 (*3) | C_154823200_10 | 100% (7 samples in triplicate) | 100% (7 samples in triplicate) | Yes | 100% (24 samples) | Yes | 100% (95% CI, 65–100) | 100% (95% CI, 96–100) |
| rs186364861 (*5) | C_181955856_10 | ||||||||
| SBF2 | rs7102464 | C__29019176_10 | 100% (14 samples in triplicate) | 100% (18 samples in triplicate) | Yes | 100% (12 samples and an additional 9 samples from another laboratory) | Yes | 100% (95% CI, 81–100) | 100% (95% CI, 98–100) |
| rs146987383 | C_161447122_10 | ||||||||
| rs141368249 | C_161190467_10 | ||||||||
| rs117957652 | C_152435684_10 | ||||||||
| rs149501654 | C_161562183_10 | ||||||||
| SEMA3C | rs7779029 | C____334680_10 | 100% (14 samples in triplicate) | 100% (18 samples in triplicate) | Yes | 100% (12 samples) | Yes | 100% (95% CI, 78–100) | 100% (95% CI, 89–100) |
| rs11979430 | C___2621121_10 | ||||||||
| SLC16A5 | rs4788863 | C____156080_10 | 100% (7 samples in triplicate) | 100% (7 samples in triplicate) | Yes | 100% (16 samples) | Yes | 100% (95% CI, 85–100) | 100% (95% CI, 72–100) |
| SLC28A3 | rs885004 | C___2752627_10 | 100% (14 samples in triplicate) | 100% (18 samples in triplicate) | Yes | 100% (11 samples) | Yes | 100% (95% CI, 70–100) | 100% (95% CI, 90–100) |
| rs7853758 | C___1820227_30 | ||||||||
| SOD2 | rs4880 | C___8709053_10 | 100% (7 samples in triplicate) | 100% (7 samples in triplicate) | Yes | 100% (8 samples) | Yes | 100% (95% CI, 44–100) | 100% (95% CI, 77–100) |
| TLR4 | rs4986790 | C__11722238_20 | 100% (14 samples in triplicate) | 100% (18 samples in triplicate) | Yes | 100% (12 samples) | Yes | 100% (95% CI, 21–100) | 100% (95% CI, 86–100) |
| TPMT | rs12201199 | C__31923406_10 | 100% (7 samples in triplicate) | 100% (7 samples in triplicate) | Yes | 100% (16 samples) | Yes | 100% (95% CI, 70–100) | 100% (95% CI, 86–100) |
∗
Robustness means obtaining the same genotyping result using two different instruments on different days and using input DNA within a concentration range of 15.4 to 50.8 ng/μL.