Abstract PS2-07-30: Structural Variants in Homologous Recombination Repair/DNA Damage Response Pathways as an Alternative Mechanism of Genomic Instability in Breast Cancer

Abstract Background: Alterations in homologous recombination repair (HRR) and DNA damage response (DDR) pathways drive genomic instability in a subset of breast cancers (BC), with associated therapeutic implications. While inactivating mutations in HRR/DDR genes are well established, the role of structural variants (SVs) disrupting these pathways remains to be determined. Here, through the analysis of a large cohort of BC, we sought to investigate SVs as a mechanism of HRR/DDR gene inactivation and to assess their contribution to genomic instability through homologous recombination deficiency (HRD) genomic scars and mutational signatures. Methods: We interrogated 9,481 BCs (n=4,376 primary; n=5,105 metastasis), previously subjected to clinical tumor/normal targeted sequencing (MSK-IMPACT), to identify SVs affecting the HRR/DDR core genes BRCA1, BRCA2, PALB2, ATM and CHEK2. Loss of heterozygosity of the wild-type allele (LOH) was assessed using FACETS, and the driver probability of fusion genes was evaluated using Oncofuse. Mutational signatures were inferred using SigMA and HRD status was assessed though evaluation of genomic scars by applying an algorithm tailored for MSK-IMPACT data. Results: We identified 58 BCs (n=21 primary; n=37 metastasis) harboring SVs affecting the HRD/DDR genes interrogated, including ATM (n=14), BRCA1 (n=14), BRCA2 (n=18), CHEK2 (n=6) and PALB2 (n=6). The SVs included fusion genes (n=34), deletions (n=16), duplications (n=14) and inversions (n=4). Most SVs (67%; 39/58) were out-of-frame, while 33% (19/58) were in-frame. Bi-allelic inactivation was identified in 55% (26/47) of evaluable cases, in the form of LOH (81%; 21/26) or as a second somatic mutation (19%; 5/26). Among fusion genes, half (17/34) had an Oncofuse driver probability >50%, suggesting that they were likely drivers. BCs with SVs in the HRR genes BRCA1, BRCA2 and PALB2 were classified as HRD in 55%, 82% and 83% of cases, respectively, and showed a dominant HRD-associated mutational signature 3 in 64%, 65% and 50% of cases, respectively. Conversely, BCs with DDR genes CHEK2 and ATM SVs were classified as non-HRD in 60% and 57% of cases, respectively, exhibiting predominantly clock (42% and 60%) and APOBEC (40% and 25%) mutational signatures. Conclusions: We demonstrate that although rare, SVs in core HRR/DDR genes represent an underrecognized mechanism of gene inactivation in a subset of BCs. Notably, their associated HRD genomic scars and mutational signatures mirror those observed in cases harboring inactivating mutations in those genes, supporting the functional relevance of these SVs in shaping HRR/DDR related processes. Our findings highlight alternative mechanisms driving genomic instability, deepen our understanding of the HRR/DDR pathways in BC, and broaden the potential eligibility for targeted therapies exploiting DNA repair deficiencies. Citation Format: A. Da Cruz Paula, D. Muldoon, A. Gazzo, M. Repetto, C. Schwartz, H. Dopeso, D. Ross, H. Wen, H. Zhang, L. Norton, E. Brogi, C. Bandlamudi, B. Weigelt, F. Pareja. Structural Variants in Homologous Recombination Repair/DNA Damage Response Pathways as an Alternative Mechanism of Genomic Instability in Breast Cancer [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 PS2-07-30.