TABLE 4.
Quality Control for FastIDH Assay
| Run ID | Index | Sample | Result (If Available) | c.395A Count (R132H) | Total Read Count | VAF c.395G>A (R132H) |
|---|---|---|---|---|---|---|
| FR124 | i30 | Neg. contr. fr. DNA | 0 | 0 | NA | |
| FR124 | i31 | Positive control 1 | IDH1 R132H | 1990 | 6078 | 32.7% |
| FR124 | i32 | Neg. contr. fr. DNA | 1 | 7 | NA | |
| FR124 | i33 | Positive control 1 | IDH1 R132H | 1695 | 5294 | 32.0% |
| FR124 | i35 | Neg. contr. fr. DNA | 0 | 0 | NA | |
| FR124 | i36 | Positive control 1 | IDH1 R132H | 1853 | 5663 | 32.7% |
| FR124 | i38 | Wt control 1 | wt | 5 | 4258 | 0.1% |
| FR124 | i41 | Neg. contr. fr. DNA | 3 | 4 | NA | |
| FR124 | i42 | Positive control 1 | wt | 2352 | 7490 | 31.4% |
| FR122 | i30 | Wt control 2 | wt | 7 | 3569 | 0.2% |
| FR122 | i32 | Positive control 1 | IDH1 R132H | 1290 | 3994 | 32.3% |
| FR122 | i36 | Wt control 2 | wt | 3 | 1268 | 0.2% |
| FR122 | i38 | Positive control 1 | IDH1 R132H | 1539 | 4829 | 31.9% |
| FR122 | i36 | Wt control 2 | wt | 7 | 4761 | 0.1% |
| FR122 | i42 | Positive control 1 | IDH1 R132H | 1651 | 5077 | 32.5% |
| FR122 | i31 | Neg. contr. no template | 0 | 15 | NA | |
| FR122 | i33 | Neg. contr. no template | 0 | 0 | NA | |
| FR122 | i35 | Neg. contr. no template | 0 | 0 | NA | |
| FR120 | i30 | Neg. contr. no template | 1 | 5 | NA | |
| FR120 | i31 | Neg. contr. no template | 0 | 7 | NA | |
| FR120 | i32 | Neg. contr. no template | 0 | 0 | NA | |
| FR120 | i33 | Neg. contr. no template | 0 | 1 | NA | |
| FR120 | i35 | Neg. contr. no template | 0 | 0 | NA | |
| FR120 | i36 | Positive control 2 | IDH1 R132H | 5744 | 14602 | 39% |
| FR120 | i38 | Positive control 1 | IDH1 R132H | 4702 | 15031 | 31% |
| FR120 | i41 | Wt control 3 | wt | 26 | 17907 | 0.1% |
| FR120 | i42 | Wt control 4 | wt | 18 | 15300 | 0.1% |
| Average c.395A count | Aver. total read count | VAF average +-SD | ||||
| DH1 R132H positive control 1 (n=8) | 2134 | 6131 | 32.1%±0.6% | |||
| Wt controls (n=6) | 8 | 12259 | 0.17%±0.04% | |||
| Negative control: no template/fr. DNA (n=12) | 0.2 | 3.1 | NA |
Data from 3 independent runs were used.
For negative control with fragmented DNA we used ultrasound fragmented donor blood DNA with median fragment size <100 bp.
For no template control on DNA library was added to the sequencer in order to see the contamination based on index hopping and/or sequencer overflow.
DNA isolated from glial tumor tissue with known IDH1/2 status was used as positive control and wt control.
IDH indicates isocitrate dehydrogenase 1; NA, not analyzable; VAF, variant allele fraction; wt, wild type.