Assessing the value of incorporating a polygenic risk score with non-genetic factors for predicting breast cancer diagnosis in the UK Biobank

Abstract

Background: Previous studies have demonstrated that incorporating a polygenic risk score (PRS) to existing risk prediction models for breast cancer improves model fit, but to determine its clinical utility the impact on risk categorisation needs to be established. We add a PRS to two well-established models and quantify the difference in classification using the net reclassification improvement (NRI). Methods: We analysed data from 126,490 post-menopausal women of “White British” ancestry, aged 40-69 years at baseline from the UK Biobank prospective cohort. The breast cancer outcome was derived from linked registry data and hospital records. We combined a PRS for breast cancer with 10-year risk scores from the Tyrer-Cuzick and Gail models, and compared these to the risk scores from the models using phenotypic variables alone. We report metrics of discrimination and classification, and consider the importance of the risk threshold selected. Results: The Harrell’s C statistic of the 10-year risk from the Tyrer-Cuzick and Gail models was 0.57 and 0.54, respectively, increasing to 0.67 when the PRS was included. Inclusion of the PRS gave a positive NRI for cases in both models (0.080 (95% confidence interval: 0.053, 0.104) and 0.051 (95% CI: 0.030, 0.073), respectively), with negligible impact on controls. Conclusions: The addition of a PRS for breast cancer to the well-established Tyrer-Cuzick and Gail models provides a substantial improvement in the prediction accuracy and risk stratification. Impact: These findings could have important implications for the ongoing discussion about the value of PRS in risk prediction models and screening.