Validity of models for predicting BRCA1 and BRCA2 mutations

Abstract

Background: Deleterious mutations of the BRCA1 and BRCA2 genes confer susceptibility to breast and ovarian cancer. At least 7 models for estimating the probabilities of having a mutation are used widely in clinical and scientific activities; however, the merits and limitations of these models are not fully understood.

Objective: To systematically quantify the accuracy of the following publicly available models to predict mutation carrier status: BRCAPRO, family history assessment tool, Finnish, Myriad, National Cancer Institute, University of Pennsylvania, and Yale University.

Design: Cross-sectional validation study, using model predictions and BRCA1 or BRCA2 mutation status of patients different from those used to develop the models.

Setting: Multicenter study across Cancer Genetics Network participating centers.

Patients: 3 population-based samples of participants in research studies and 8 samples from genetic counseling clinics.

Measurements: Discrimination between individuals testing positive for a mutation in BRCA1 or BRCA2 from those testing negative, as measured by the c-statistic, and sensitivity and specificity of model predictions.

Results: The 7 models differ in their predictions. The better-performing models have a c-statistic around 80%. BRCAPRO has the largest c-statistic overall and in all but 2 patient subgroups, although the margin over other models is narrow in many strata. Outside of high-risk populations, all models have high false-negative and false-positive rates across a range of probability thresholds used to refer for mutation testing.

Limitation: Three recently published models were not included.

Conclusions: All models identify women who probably carry a deleterious mutation of BRCA1 or BRCA2 with adequate discrimination to support individualized genetic counseling, although discrimination varies across models and populations.

Figure 1. C-statistic, by age of the counselee and model

Points within age groups are slightly spaced horizontally for readability. Vertical bars are 95% CIs. A description of each model is given in Table 3. FHAT = family history assessment tool; NCI = National Cancer Institute; Penn = University of Pennsylvania; Yale = Yale University.