TABLE 3.
Correlation, precision, and recall between TMB computed with WES and 389 genes panel using thresholds 20mut/Mb for each cancer except dbGaP where the threshold was 10 mut/Mb.
| Pearson correlation | Pearson H-TMB | Pearson L-TMB | PPV | TPR | TNR | NPV | TP | FP | TN | FN | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Genentech | 0.94 | 0.95 | 0.87 | 1 | 1 | 1 | 1 | 2 | 0 | 11 | 0 |
| Colonomics | 0.69 | - | 0.69 | - | - | - | - | - | - | 8 | - |
| Li-JP | 0.99 | 0.99 | 0.73 | 0.87 | 0.87 | 0.68 | 0.68 | 42 | 6 | 13 | 6 |
| TCGA 126 COAD | 0.97 | 0.95 | 0.85 | 0.75 | 1 | 0.95 | 1 | 3 | 1 | 20 | 0 |
| dbGap* | 0.89 | 1 | 0.86 | - | 0 | 1 | 0.95 | 0 | 0 | 18 | 1 |
| COCA | 0.99 | 0.99 | 0.80 | 0.89 | 0.62 | 1 | 0.94 | 5 | 0 | 50 | 3 |
The table also reports the True Negative Rate, Negative Predicted Value, and the confusion matrix for each cancer type.