Exome-Wide Association Analysis Identifies Rare Germline Susceptibility Variants in Early-Onset Breast Cancer Among Saudi Women

Early-onset breast cancer (EOBC) is disproportionately common in Saudi Arabia, where women present nearly a decade earlier than in Western countries, suggesting unique inherited susceptibility. While BRCA1/2 explain part of the hereditary risk, the contribution of rare coding variants in Arab EOBC remains unclear. Whole-exome sequencing was performed on germline DNA from 102 unrelated Saudi EOBC patients and 1395 cancer-free controls recruited from the same national Saudi cohort. Rare variants were defined by stringent frequency and quality thresholds and classified as rare loss-of-function (RLOF) or rare predicted damaging variants (RPDVs). Gene-level case–control analyses were conducted using burden tests, with exome-wide significance set at p < 2.5 × 10−6. RLOF variants in BRCA1 (6.9% of EOBC vs. 0.14% of controls; OR = 51.3; p < 1.0 × 10−10) and RPDVs in TP53 (4.9% vs. 0.36%; OR = 14.3; p = 5.39 × 10−8) demonstrated strong associations. Sequence Kernel Association Test (SKAT) analysis identified NOTCH4 and OR12D3 and reinforced burden-based significance in GUCY2F, FRMPD3, and SHROOM2. No enriched signaling pathway emerged, indicating heterogeneous rare-variant mechanisms. This first germline exome-wide rare-variant association study in Saudi EOBC identifies substantial enrichment driven by BRCA1, TP53, and additional candidate genes, supporting population-specific genetic risk evaluation and the need for replication in larger Arab cohorts.