Table 4.
Performance measures for each model at the 10% or 20% threshold for BRCA1/2 mutation carrier probability.
| Carrier number/rate | Test parameters at set threshold | |||||
|---|---|---|---|---|---|---|
| Entire cohort | ||||||
| 10% threshold | <10% | ≥10% | Sensitivity | Specificity | PPV | NPV |
| BOADICEA | 26/583 | 22/64 | 0.46 | 0.93 | 0.34 | 0.96 |
| BRCAPRO | 14/370 | 34/277 | 0.71 | 0.59 | 0.12 | 0.96 |
| Myriad | 25/526 | 23/121 | 0.48 | 0.84 | 0.19 | 0.95 |
| Penn II | 9/239 | 41/408 | 0.82 | 0.39 | 0.10 | 0.96 |
| 20% threshold | <20% | ≥20% | Sensitivity | Specificity | PPV | NPV |
| BOADICEA | 32/612 | 16/35 | 0.33 | 0.97 | 0.46 | 0.95 |
| BRCAPRO | 19/474 | 29/173 | 0.60 | 0.76 | 0.17 | 0.96 |
| Myriad | 37/612 | 11/35 | 0.23 | 0.96 | 0.31 | 0.94 |
| Penn II | 36/584 | 12/63 | 0.25 | 0.91 | 0.19 | 0.94 |
| BC/OC(−)FH(+) subgroup | ||||||
| 10% threshold | <10% | ≥10% | Sensitivity | Specificity | PPV | NPV |
| Tyrer-Cuzick | 2/134 | 4/10 | 0.67 | 0.96 | 0.40 | 0.99 |
| BOADICEA | 1/136 | 5/8 | 0.83 | 0.98 | 0.62 | 0.99 |
| BRCAPRO | 1/97 | 5/47 | 0.83 | 0.70 | 0.11 | 0.99 |
| Myriad | 6/144 | 0/0 | 0.00 | 1.00 | NaN | 0.96 |
| Penn II | 3/28 | 3/116 | 0.50 | 0.18 | 0.03 | 0.89 |
| 20% threshold | <20% | ≥20% | Sensitivity | Specificity | PPV | NPV |
| Tyrer-Cuzick | 4/141 | 2/3 | 0.33 | 0.99 | 0.67 | 0.97 |
| BOADICEA | 4/141 | 2/3 | 0.33 | 0.99 | 0.67 | 0.97 |
| BRCAPRO | 1/112 | 5/32 | 0.83 | 0.80 | 0.16 | 0.99 |
| Myriad | 6/144 | 0/0 | 0.00 | 1.00 | NaN | 0.96 |
| Penn II | 6/142 | 0/2 | 0.00 | 0.99 | 0.00 | 0.96 |
| BC/OC(+)FH(+) subgroup | ||||||
| 10% threshold | <10% | ≥10% | Sensitivity | Specificity | PPV | NPV |
| BOADICEA | 11/196 | 14/45 | 0.56 | 0.86 | 0.31 | 0.94 |
| BRCAPRO | 3/94 | 22/147 | 0.88 | 0.42 | 0.15 | 0.97 |
| Myriad | 7/145 | 18/96 | 0.72 | 0.64 | 0.19 | 0.95 |
| Penn II | 2/59 | 23/182 | 0.92 | 0.26 | 0.13 | 0.97 |
| 20% threshold | <20% | ≥20% | Sensitivity | Specificity | PPV | NPV |
| BOADICEA | 13/212 | 12/29 | 0.48 | 0.92 | 0.41 | 0.94 |
| BRCAPRO | 4/134 | 21/107 | 0.84 | 0.60 | 0.20 | 0.97 |
| Myriad | 16/208 | 9/33 | 0.36 | 0.89 | 0.27 | 0.92 |
| Penn II | 16/202 | 9/39 | 0.36 | 0.86 | 0.23 | 0.92 |
| BC/OC(+)FH(−) subgroup | ||||||
| 10% threshold | <10% | ≥10% | Sensitivity | Specificity | PPV | NPV |
| BOADICEA | 14/253 | 3/9 | 0.18 | 0.98 | 0.33 | 0.94 |
| BRCAPRO | 10/180 | 7/82 | 0.41 | 0.69 | 0.09 | 0.94 |
| Myriad | 12/237 | 5/25 | 0.29 | 0.92 | 0.20 | 0.95 |
| Penn II | 4/64 | 13/198 | 0.76 | 0.24 | 0.07 | 0.94 |
| 20% threshold | <20% | ≥20% | Sensitivity | Specificity | PPV | NPV |
| BOADICEA | 15/259 | 2/3 | 0.12 | 1.00 | 0.67 | 0.94 |
| BRCAPRO | 14/228 | 3/34 | 0.18 | 0.87 | 0.09 | 0.94 |
| Myriad | 15/260 | 2/2 | 0.12 | 1.00 | 1.00 | 0.94 |
| Penn II | 14/240 | 3/22 | 0.18 | 0.92 | 0.14 | 0.94 |
PPV: positive predictive value; NPV: negative predictive value; NaN: not a number