Potential advantage of clinical exome sequencing in <i>BRCA1/2</i>-negative families: a retrospective study of a cohort of 500 patients at a high-risk for hereditary cancers.

Abstract

Hereditary cancer syndromes (HCSs) account for approximately 5-10% of all cancers and are frequently associated with pathogenic variants (PVs) in genes such as <i>BRCA1</i> and <i>BRCA2</i>. Nevertheless, a substantial proportion of individuals with strong familial cancer aggregation remain genetically unexplained after standard multigene panel testing. Clinical exome sequencing (CES) may overcome this limitation by enabling a broader exploration of cancer susceptibility genes. This retrospective study included 500 high-risk patients who previously tested negative for <i>BRCA1/2</i> PVs. All samples were analysed using next-generation sequencing technology. Initially, a 60-gene filtered panel recommended by the American Society of Clinical Oncology (ASCO) guidelines was applied, followed by a 102-gene filtered panel derived from CES to identify additional PVs or likely PVs (LPVs) beyond current diagnostic panels. Variant classification was performed according to the American College of Medical Genetics and Genomics/Association for Molecular Pathology guidelines, incorporating ClinGen and gene-specific expert curation recommendations when available. Within the ASCO panel, PV/LPVs were identified in 9% of patients while 35% carried variants of uncertain significance. CES identified additional PVs/LPVs in 5% of patients in genes not currently included in ASCO-recommended surveillance panels, such as <i>RAD50</i>, <i>BLM</i>, <i>WRN</i>, <i>PMS1</i> and <i>FANCA</i>. These variants may represent candidate susceptibility loci requiring further clinical and functional validation. CES may provide additional exploratory genomic information in selected high-risk <i>BRCA1/2</i>-negative patients, particularly when standard panel testing is uninformative. Although many of the additional findings identified are not yet clinically actionable, CES represents a valuable resource for future reinterpretation as gene-disease evidence evolves. Overall, our findings support the use of CES as a second-tier exploratory approach in carefully selected high-risk cases, while emphasising the need for cautious interpretation and continued gene-disease curation.