Abstract 6274: Novel candidate breast cancer predisposing genes identified in high-risk Brazilian families.

Abstract It is estimated that 5 to 10% of breast cancer cases have an important hereditary component. Individuals at high risk often present multiple affected relatives, early onset, bilateral disease, or triple-negative tumors. These patients usually undergo next-generation sequencing (NGS) panels targeting well-established predisposing genes such as BRCA1 and BRCA2. However, pathogenic or likely pathogenic (P/LP) variants are identified in fewer than 30% of such cases, the majority lack a clear genetic etiology. Given the large fraction without a known causal variant and the limited representation of Brazilian families in genomic databases, we performed whole-exome sequencing (WES) in multiple families to search for novel breast cancer predisposing genes. We included families with at least three breast cancer diagnoses whose probands previously tested negative for P/LP variants in well-established predisposing genes (IRB: 25325019.5.0000.5464). WES was performed in 29 affected women from eight families (median per family = 3.6) using DNA extracted from blood. Libraries were prepared with the xGen Exome v2 kit (IDT) and sequenced on the Illumina HiSeq 2500. Variant annotation and prioritization were performed using VarSeq (Golden Helix). After quality filtering, we prioritized predicted high-impact variants based on complete segregation across affected relatives and gene functions relevant to cancer biology, identifying 26 rare variants in 26 candidate genes. For the most promising genes, we assessed the loss of heterozygosity (LOH) at the mutated locus in available FFPE tumors using deep amplicon-based NGS. Two candidate genes identified in separate families stood out due to harboring predicted high-impact variants and their participation in signaling pathways and cellular processes implicated in cancer, the tumor suppressors RAD54L2 and SMARCA4. RAD54L2 participates in the homologous recombination DNA repair pathway, which encompasses several well-established breast cancer predisposing genes, including BRCA1, BRCA2, and CHEK2. Among the four affected carriers of the RAD54L2 variant, tumor tissue was available from two, and one showed LOH of the mutated locus, supporting a second-hit mechanism. SMARCA4, a core component of the SWI/SNF chromatin-remodeling complex, is essential for genome stability and DNA damage response. It is also known as a predisposing gene for rhabdoid tumors and small cell carcinoma of the ovary, though not for breast cancer. Tumor samples from two sisters with bilateral disease revealed LOH of the mutated locus in one case. These results have the potential to deepen the genetic landscape of hereditary breast cancer by identifying novel candidate genes for functional investigation and future clinical validation. They also underscore the relevance of studying Brazilian and Latin American families, populations still underrepresented in global genomic studies. Citation Format: Gabriel Bandeira do Carmo, Sara Ferreira Pires, Elisa Helena Farias Jandrey, Neda Zamani, Katia Maria da Rocha, Karina Miranda Santiago, Rafael Canfield Brianese, Jaqueline Yu Wang, Giovana Tardin Torrezan, Edenir Inez Palmero, Steven Narod, Mayana Zatz, Thomaz Rafael Gollop, Dirce Maria Carraro, Ana Cristina Victorino Krepischi, Mohammad Reza Akbari, Oswaldo Keith Okamoto. Novel candidate breast cancer predisposing genes identified in high-risk Brazilian families [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 6274.