Table 4.
Contingency Table of FGFR1 Amplification Calls as Determined by Call-FGFR1-Amp against the FISH Gold Standards in the UBC-TAM Cohort
| Call-FGFR1-amp | Total N | FISH |
P value | κ | |
|---|---|---|---|---|---|
| Nonamplified | Amplified | ||||
| Nonamplified | 500 | 497 | 3 | 4.11E-63 | 0.78 |
| Amplified | 100 | 30 | 70 | ||
| Total N | 600 | 527 | 73 | ||
| Specificity | Sensitivity | NPV | PPV | Accuracy | Youden | Youden* | FP/TP | FN/TN |
|---|---|---|---|---|---|---|---|---|
| 0.94 | 0.96 | 0.99 | 0.7 | 0.95 | 0.9 | 0.96 | 0.43 | 0.01 |
Call-FGFR1-amp captures almost all of the FGFR1-amplified cases and results in a high sensitivity, specificity, NPV, and overall accuracy (Materials and Methods provides definitions of the diagnostic measures).
FISH, fluorescent in situ hybridization; FN, false negative; FP, false positive; NPV, negative predictive value; PPV, positive predictive value; TN, true negative, TP, true positive; UBC-TAM, University of British Columbia–tamoxifen; 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.