Table 3.
Contingency Table of FGFR1 Amplification Calls as Determined by Call-FGFR1-amp against the FISH Gold Standards in the SPECS Cohort
| Call-FGFR1-amp | Total no. | FISH |
P value | κ | |
|---|---|---|---|---|---|
| Nonamplified | Amplified | ||||
| Non-amplified | 35 | 35 | 0 | 4.59E-06 | 0.83 |
| Amplified | 8 | 2 | 6 | ||
| Total no. | 43 | 37 | 6 | ||
| Specificity | Sensitivity | NPV | PPV | Accuracy | Youden | Youden* | FP/TP | FN/TN |
|---|---|---|---|---|---|---|---|---|
| 0.95 | 1 | 1 | 0.75 | 0.95 | 0.95 | 1 | 0.33 | 0 |
Call-FGFR1-amp captures all FGFR1-amplified cases and results in a high sensitivity, specificity, NPV, and overall accuracy.
FISH, fluorescent in situ hybridization; FN, false negative; FP, false positive; NPV, negative predictive value; PPV, positive predictive value; SPECS, Strategic Partnering to Evaluate Cancer Signatures; TN, true negative, TP, true positive; Youden, does not consider population prevalence and uses equal weight on sensitivity and specificity; Youden*, considers population prevalence and allows different penalty/cost on FP and FN.