Table 2 Sensitivity and specificity calculations for all SMs compared, and overall. These calculations include all samples passing and failing QC, and all SMs, no matter what SM score
SM | TN | FN | TP | FP | Sensitivity | Sensitivity.n | Specificity | Specificity.n |
|---|---|---|---|---|---|---|---|---|
BRAF:p.G469A:c.1406G > C | 2 | 0 | 2 | 1 | 0.67 | 3 | 1.00 | 2 |
BRAF:p.G469E:c.1406G > A | 4 | 0 | 0 | 1 | 0.00 | 1 | 1.00 | 4 |
BRAF:p.V600E:c.1799 T > A | 25 | 0 | 22 | 0 | 1.00 | 22 | 1.00 | 25 |
BRAF:p.V600K:c.1798_1799GT > AA | 46 | 0 | 1 | 0 | 1.00 | 1 | 1.00 | 46 |
EGFR:p.G719A:c.2156G > C | 6 | 0 | 0 | 0 | NA | 0 | 1.00 | 6 |
EGFR:p.G719C:c.2155G > T | 1 | 0 | 0 | 5 | 0.00 | 5 | 1.00 | 1 |
EGFR:p.G719S:c.2155G > A | 4 | 0 | 0 | 2 | 0.00 | 2 | 1.00 | 4 |
EGFR:p.L858R:c.2573 T > G | 19 | 0 | 0 | 0 | NA | 0 | 1.00 | 19 |
EGFR:p.L861Q:c.2582 T > A | 17 | 0 | 1 | 1 | 0.50 | 2 | 1.00 | 17 |
EGFR:p.T790M:c.2369C > T | 1 | 0 | 1 | 0 | 1.00 | 1 | 1.00 | 1 |
IDH2:p.R140Q:c.419G > A | 1 | 0 | 0 | 2 | 0.00 | 2 | 1.00 | 1 |
KRAS:p.G12C/S:c.34G > T/A | 81 | 0 | 22 | 0 | 1.00 | 22 | 1.00 | 81 |
KRAS:p.G12D/V:c.35G > A/T | 80 | 1 | 22 | 0 | 1.00 | 22 | 0.99 | 81 |
KRAS:p.G13D:c.38G > A | 81 | 0 | 22 | 0 | 1.00 | 22 | 1.00 | 81 |
KRAS:p.Q61H:c.183A > C | 6 | 0 | 2 | 4 | 0.33 | 6 | 1.00 | 6 |
KRAS:p.Q61H:c.183A > T | 9 | 1 | 1 | 1 | 0.50 | 2 | 0.90 | 10 |
KRAS:p.Q61K/K:c.180_181TC > TA/AA | 11 | 0 | 1 | 0 | 1.00 | 1 | 1.00 | 11 |
NRAS:p.G12D:c.35G > A | 27 | 0 | 4 | 5 | 0.44 | 9 | 1.00 | 27 |
NRAS:p.G12S/C:c.34G > A/T | 29 | 1 | 5 | 1 | 0.83 | 6 | 0.97 | 30 |
NRAS:p.G12V:c.35G > T | 36 | 0 | 0 | 0 | NA | 0 | 1.00 | 36 |
NRAS:p.Q61K:c.181C > A | 29 | 0 | 4 | 0 | 1.00 | 4 | 1.00 | 29 |
NRAS:p.Q61L:c.182A > T | 32 | 0 | 1 | 0 | 1.00 | 1 | 1.00 | 32 |
NRAS:p.Q61R:c.182A > G | 25 | 0 | 5 | 3 | 0.63 | 8 | 1.00 | 25 |
PIK3CA:p.E542K:c.1624G > A | 18 | 0 | 22 | 0 | 1.00 | 22 | 1.00 | 18 |
PIK3CA:p.E545K:c.1633G > A | 23 | 1 | 16 | 0 | 1.00 | 16 | 0.96 | 24 |
PIK3CA:p.H1047L:c.3140A > T | 46 | 0 | 0 | 0 | NA | 0 | 1.00 | 46 |
PIK3CA:p.H1047R:c.3140A > G | 29 | 1 | 13 | 3 | 0.81 | 16 | 0.97 | 30 |
PIK3CA:p.Q546K:c.1636C > A | 38 | 0 | 2 | 0 | 1.00 | 2 | 1.00 | 38 |
PTEN:p.R130*:c.388C > T | 1 | 0 | 0 | 0 | NA | 0 | 1.00 | 1 |
PTEN:p.R130G:c.388C > G | 0 | 0 | 0 | 1 | 0.00 | 1 | NA | 0 |
PTEN:p.R130Q/fs*4:c.389G > A/delG | 1 | 0 | 0 | 0 | NA | 0 | 1.00 | 1 |
PTEN:p.R159S:c.477G > T | 6 | 0 | 0 | 2 | 0.00 | 2 | 1.00 | 6 |
TP53:p.C176F:c.527G > T | 47 | 0 | 7 | 0 | 1.00 | 7 | 1.00 | 47 |
TP53:p.G245S/C:c.733G > A/T | 31 | 1 | 15 | 2 | 0.88 | 17 | 0.97 | 32 |
TP53:p.H179R:c.536A > G | 50 | 0 | 1 | 3 | 0.25 | 4 | 1.00 | 50 |
TP53:p.R175H:c.524G > A | 33 | 0 | 21 | 0 | 1.00 | 21 | 1.00 | 33 |
TP53:p.R196*:c.586C > T | 0 | 0 | 10 | 0 | 1.00 | 10 | NA | 0 |
TP53:p.R213*:c.637C > T | 16 | 0 | 15 | 2 | 0.88 | 17 | 1.00 | 16 |
TP53:p.R248Q/L:c.743G > A/T | 21 | 1 | 27 | 0 | 1.00 | 27 | 0.95 | 22 |
TP53:p.R248W:c.742C > T | 47 | 1 | 1 | 0 | 1.00 | 1 | 0.98 | 48 |
TP53:p.R249S:c.747G > T | 46 | 0 | 2 | 1 | 0.67 | 3 | 1.00 | 46 |
TP53:p.R282W:c.844C > T | 45 | 1 | 13 | 0 | 1.00 | 13 | 0.98 | 46 |
TP53:p.R306*:c.916C > T | 14 | 0 | 13 | 0 | 1.00 | 13 | 1.00 | 14 |
TP53:p.V157F:c.469G > T | 4 | 0 | 3 | 0 | 1.00 | 3 | 1.00 | 4 |
TP53:p.Y163C:c.488A > G | 3 | 0 | 3 | 1 | 0.75 | 4 | 1.00 | 3 |
TP53:p.Y220C:c.659A > G | 30 | 0 | 2 | 1 | 0.67 | 3 | 1.00 | 30 |
Totals | 1121 | 9 | 302 | 42 | 0.88 | 344 | 0.99 | 1130 |