Abstract P6-08-07: Polygenic breast cancer risk modification in carriers of high and intermediate risk gene mutations
Authors: Gallagher Shannon , Hughes Elisha , Wagner Susanne , Tshiaba Placede , Rosenthal Eric , Roa Benjamin B. , Kurian Allison , Domchek Susan , Garber Judy , Lancaster Johnathan M. , Weitzel Jeffrey , Gutin Alexander , Lanchbury Jerry S. , Robson Mark 
Published: March 2020

Abstract
Background: The incorporation of polygenic scores into breast cancer risk assessment models has led to improved risk management for women of European ancestry. However, few studies have examined the extent to which polygenic scores modify risk for carriers of breast cancer susceptibility gene mutations. Current literature suggests that a 77-SNP polygenic score developed from large, mainly non-carrier general population studies can stratify breast cancer risk for carriers of the CHEK2 founder mutation 1100delC with the same effect size observed for non-carriers. Consequently, several groups have modified risk estimates for carriers of other pathogenic variants by applying published effect estimates from non-carriers. In a recent study, a similar 88-SNP polygenic score showed reduced effectiveness in BRCA1 and BRCA2 carriers compared to non-carriers. This highlights the need for more information on polygenic score performance among women who carry pathogenic variants in ATM or PALB2, or in CHEK2 other than the 1100delC founder mutation. We previously described an 86-SNP polygenic residual risk score (RRS) that characterizes genetic risk which is not due to high- or moderate-penetrance breast cancer gene mutations. Here, we present pre-specified independent validation of the RRS for BRCA1, BRCA2, CHEK2, ATM and PALB2 carriers.Methods: This IRB-approved study included 152,172 women of European ancestry who were tested clinically for hereditary cancer risk with a multi-gene panel. The RRS was evaluated separately for carriers of BRCA1 (N=2,249), BRCA2 (N=2,638), CHEK2 (N=2,564), ATM (N=1,445) and PALB2 (N=906), and for mutation-free women (N=141,160). Clinical information was obtained from test requisition forms. Multivariable logistic regression was used to examine the association of RRS with invasive breast cancer after accounting for age and family cancer history. Effect sizes, expressed as standardized odds ratios (ORs) with 95% confidence intervals (CIs), were assessed for carriers of each gene and for non-carriers. Results: RRS was strongly associated with breast cancer risk in each of the BRCA1, BRCA2, CHEK2, ATM and PALB2 carrier populations (p&lt;10−4). Risk modification in CHEK2 carriers (OR 1.49; CI 1.36-1.64) was consistent with that observed in non-carriers (OR 1.47; CI 1.45-1.49). CHEK2 carriers in the highest RRS quintile had approximately 1.7-fold higher risk than the middle quintile (OR 1.67; CI 1.26 - 2.20), and the lowest quintile had risk lowered by factor of 0.59 (OR 0.59; CI 0.44 - 0.80). We observed reduced modification similar to existing literature for carriers of BRCA1 (OR 1.20; CI 1.10-1.32) and BRCA2 (OR 1.23; CI 1.12-1.34). Odds ratios for ATM (1.37; CI 1.21-1.55) and PALB2 (1.34; CI 1.16-1.55) had wide confidence intervals that overlapped those for the other carrier populations. Discussion: The RRS significantly modifies risk for carriers of BRCA1, BRCA2, CHEK2, ATM and PALB2 mutations albeit with apparently different effect sizes. These results indicate that risk estimates employing polygenic scores may need to be derived separately for each gene. Given the modest effect on BRCA1 and BRCA2 risk and the substantial risks conferred by these genes even with lower RRS, the clinical implications of polygenic modification in this setting are yet to be determined. In CHEK2 carriers, we observed strong polygenic modification similar to that achieved for non-carriers. For ATM and PALB2, larger studies are needed to refine polygenic effect size estimates. Comprehensive risk assessment combining RRS with family cancer history and other risk factors has potential to refine risk estimates and facilitate decision-making for women with mutations in moderate penetrance genes.
Citation Format: Shannon Gallagher, Elisha Hughes, Susanne Wagner, Placede Tshiaba, Eric Rosenthal, Benjamin B. Roa, Allison Kurian, Susan Domchek, Judy Garber, Johnathan M. Lancaster, Jeffrey Weitzel, Alexander Gutin, Jerry S. Lanchbury, Mark Robson. Polygenic breast cancer risk modification in carriers of high and intermediate risk gene mutations [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P6-08-07.