Simmons, Timothy

Abstract Background: BRCA2 variants with partially aberrant RNA splicing have been associated with a relatively lower breast cancer risk (reduced penetrance) relative to canonical pathogenic variants. However, the existence of partial loss of function (hypomorphic) missense variants, conferring reduced penetrance, is less certain. Identification and assessment of the clinical relevance of such reduced penetrance pathogenic variants (RPPVs) is needed to provide accurate risk estimates. Methods: Comprehensive functional characterization of hypomorphic missense variants (n=70) in the BRCA2 DNA-binding domain, initially identified through homology-directed DNA repair (HDR) assays, was conducted through multiple independent functional assays, including HDR, CRISPR/Cas9-based endogenous targeting, RAD51 foci formation assay, and Poly(ADP-ribose) polymerase (PARP) inhibitor response assay. Risk estimates were obtained using two large datasets from patients referred for hereditary cancer testing. A ClinGen/ACMG/AMP model was used for clinical classification. Results: The variants consistently demonstrated hypomorphic HDR activity and endogenous survival in HAP1 targeted cells, decreased RAD51 foci formation, and increased sensitivity to PARP inhibitors. These variants were associated with a moderate increase in breast cancer risk, as shown in two independent studies: one using multivariable logistic analysis adjusted for age, ancestry and family history (OR=2.41, 95%CI=1.51-3.85) and another comparing frequencies of variants in breast cancer cases to public reference controls adjusted for ancestry (OR=2.09, 95% CI=1.16-4.08). The mean age of breast cancer diagnosis for carriers of hypomorphic variants was 57 years, which was significantly older than the mean age of diagnosis of 51 years for carriers of protein truncating variants. Functional data were combined with other evidence sources in a ClinGen/ACMG/AMP model to classify 14 variants as “likely pathogenic”. Conclusions: We identified partially functional, hypomorphic missense variants associated with reduced penetrance for breast cancer. Cancer risk management guidelines for this new category of variants should be revisited given that the associated breast cancer risks warrant high risk screening but do not meet the threshold at which risk reducing mastectomy is offered. This study supports a shift in paradigm to considering variant-based risks on a continuum, with implications for risk-appropriate cancer risk management. Citation Format: H. Huang, C. Hu, J. Na, M. Kucera, T. Simmons, E. Mundt, C. C. Young, Z. Heidari, P. C. Lyra, Y. Y. Tan, K. L. Nathanson, T. Pal, R. Karam, T. Pesaran, S. Yadav, S. M. Domchek, A. N. Monteiro, E. Hughes, N. Boddicker, W. Chen, M. E. Richardson, F. J. Couch. Partially functional (hypomorphic) missense variants in BRCA2 are reduced penetrance pathogenic variants [abstract]. In: Proceedings of the San Antonio Breast Cancer Symposium 2025; 2025 Dec 9-12; San Antonio, TX. Philadelphia (PA): AACR; Clin Cancer Res 2026;32(4 Suppl):Abstract nr PD4-05.

10512 Background: Polygenic risk scores (PRSs) combine information from single-nucleotide polymorphisms (SNPs) across the genome to explain substantial genetic breast cancer (BC) susceptibility. Previous studies have demonstrated that a multiple-ancestry PRS (MA-385) based on 56 ancestry-informative and 329 BC-associated SNPs is accurate for diverse populations and ranks among the most important known factors affecting the risk of BC development. However, medical guidelines call for more evidence before endorsing the clinical use of PRS, including studies to evaluate possible interactions of SNPs with environmental and hormonal risk factors. Here, we use longitudinal outcomes from the UK Biobank (UKB) to explore interactions of MA-385 and the five most informative individual BC-associated SNPs with the widely used Tyrer-Cuzick (TC) risk model and individual TC risk factors. Methods: The study cohort included 197,509 female UKB participants with no history of cancer at the time of study enrollment. We used Cox proportional hazards models to test associations of MA-385, individual BC SNPs, TC, and individual TC risk factors with BC outcomes. Effect modification of MA-385 and individual SNPs by clinical risk factors was evaluated by including interaction terms in the models. All models were adjusted for age at UKB enrollment and 10 principal components. Hazard ratios (HRs) and 95% confidence intervals (CIs) are reported per standard deviation, and significance tests were performed using two-sided p-values based on likelihood-ratio test statistics. Results: After a median follow-up of 11.8 years, 7,419 (3.8%) participants were diagnosed with BC.In a model including both MA-385 and TC, MA-385 was a significantly better predictor of BC development (HR = 1.56; 95% CI 1.53-1.60, p = 3.2 x 10 -329 ) over the TC model (HR = 1.21; 95% CI 1.18-1.23; p = 5.4 x 10 -69 ). We found no evidence of interaction between MA-385 and TC ( p = 0.31) , nor between individual SNPs and TC. After Bonferroni adjustment for multiple testing (102 tests), we found no evidence of interaction between MA-385 or individual SNPs with clinical TC factors. The strongest evidence for interaction was found between a BC SNP on chromosome 2 (rs13387042) and age at UKB enrollment (unadjusted p = 0.002; Bonferroni adjusted p = 0.23). Conclusions: In a longitudinal analysis of UKB, MA-385 was a highly significant predictor of BC risk and substantially improved prediction over TC. In contrast, interactions of MA-385, and individual BC SNPs, with TC and individual clinical factors in the TC model were not statistically significant. Clinical TC factors have minimal, if any, impact on the strength of the association between MA-385 and BC. These results may help to alleviate concerns expressed in guidelines that SNPs interact with environmental or hormonal risk factors.

Abstract Background: Personalized breast cancer (BC) risk assessment depends on known traditional risk factors, specific germline mutations, and genome-wide polygenic risk scores (PRS). PRS explains a substantial proportion of genetic BC susceptibility. Accuracy of BC risk prediction may be improved by combining a PRS with traditional risk factors. We recently developed and validated a 149-SNP PRS for women of diverse ancestries using ancestry-informative genetic markers and combined this with version 7 of the Tyrer-Cuzick (TC) model to generate a Combined Risk Score (CRS). Here, we describe a pre-specified prospective longitudinal clinical validation of CRS as a predictor of BC risk. Methods: Women in the U.S. who were referred for clinical genetic testing between January 2017 and February 2019 were matched to medical and hospital claims in an anonymized dataset. Women with a pathogenic mutation in a BC-related gene were excluded from analysis. Follow-up began 4 months after testing and extended to the earliest date of BC diagnosis, censoring at the time of BC preventive treatment, or November 1, 2019. Incident BC events were determined by an ICD10 code of C50.* and confirmed by relevant treatment codes. CRS calibration was evaluated by the ratio of observed (O) to expected (E) incident BCs for the full cohort, and for women split into event-based 5-year CRS risk deciles. Cox proportional hazards models were used to evaluate discriminatory accuracy in terms of hazard ratios (HR) with 95% confidence intervals (CI) and p-values from likelihood ratio chi-squared statistics. Kaplan-Meier analysis was used to examine risk for women split into high- or low-risk groups according to a 3% 5-year CRS risk threshold. Results: 130,058 women with 148,349 total patient years met study eligibility criteria and were matched to claims data. Over a median (range) follow-up of 12.1 (4.0-29.5) months, 340 incident BC events were observed. The CRS was well calibrated in the overall cohort with an O/E ratio of 1.11 (95% CI=0.99-1.23) and within deciles of predicted risk (Table). Importantly, in the highest risk decile, the O/E was 0.91 (95% CI=0.63-1.27) with CRS, but 0.67 (95% CI=0.46-0.94) with TC alone, illustrating the superior calibration of CRS. In a Cox model adjusted for age at testing, PRS had an HR per standard deviation (SD) of 1.48 (95% CI=1.33-1.64, p=2.55×10-13); the HR/SD was 1.43 (95% CI=1.29-1.59, p=1.61×10-11) after adjusting for family history. In a bivariate analysis using both CRS and TC to predict time to BC, CRS added significantly to the model after accounting for TC (HR/SD=2.89, 95% CI=2.12-3.94, p=1.20×10-11), whereas TC did not add significant information after accounting for CRS. 15,986 (12.3%) women were above the CRS high-risk threshold, including 123 with events. A total of 10,248 (7.9%) women were reclassified by the CRS model compared to the TC model. Among women who were classified as high-risk by TC, 32.6% were reclassified as low-risk by CRS; among those classified as low-risk by TC, 4.3% were reclassified as high-risk by CRS. The CRS high-risk group experienced events at over three times the rate of the low-risk group (HR=3.75, 95% CI=3.00-4.68, p=6.39×10-27). Conclusion: The CRS was well-calibrated in predicting BC and significantly improved upon a traditional risk factor model. Clinical use of the CRS may lead to improved BC prevention and screening strategies. Table: Absolute risk calibration by 5-year risk decile Incidence is reported per 1,000 women-years. 34 breast cancers were observed per decile. Citation Format: Brent Mabey, Elisha Hughes, Braden Probst, Holly J. Pederson, Timothy Simmons, Brian Morris, Brooke Hullinger, Susan Domchek, Charis Eng, Monique Gary, Jennifer Klemp, Semanti Mukherjee, Vijai Joseph, Kenneth Offit, Olufunmilayo I. Olopade, Sandhya Pruthi, Allison W. Kurian, Mark E. Robson, Pat Whitworth, Susanne Wagner, Jerry Lanchbury, Thomas Slavin, Alexander Gutin. PD14-05 Prospective longitudinal validation of a breast cancer risk prediction model in a cohort of 130,058 women [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr PD14-05.