From detection to full characterization: a germline whole-gene deletion of BRCA1 in a patient with breast cancer illustrating evolving molecular diagnostic approaches in genomics

Abstract Background: Large genomic rearrangements (LGRs), including copy number variations (CNVs), represent important molecular targets in BRCA1/2 (BRCA) testing. Although next-generation sequencing combined with dedicated bioinformatics pipelines is widely used for CNV detection, challenging cases may require an integrated approach for comprehensive genomic characterization. Methods and Results : We report a patient with breast cancer harbouring a germline deletion encompassing the entire BRCA1 gene, which was fully characterized at nucleotide-level resolution through the integration of multiple complementary molecular approaches. Germline BRCA testing was used to identify the CNV, while multiplex ligation-dependent probe amplification was performed to confirm the deletion. Whole-exome sequencing demonstrated that the deletion extended beyond BRCA1 , encompassing adjacent genomic regions. Nanopore long-read sequencing and whole-genome sequencing were subsequently used to define the deletion breakpoints, while targeted Sanger sequencing enabled their characterization at nucleotide-level resolution. To assess the presence of loss of heterozygosity at the tissue level, comprehensive genomic profiling was performed on the patient’s breast tumour. Given the unique and unusual nature of the identified CNV, we further investigated whether this genomic rearrangement could be detected in liquid biopsy using an amplicon-based BRCA testing approach. Available segregation data were suggestive of a de novo event, although this could not be conclusively demonstrated because the family study was incomplete. Conclusions : To our knowledge, this case represents the fourth documented instance worldwide of a germline whole-gene BRCA1 deletion and the first reported case in Italy. Our findings highlight the value of integrating long-read sequencing with complementary orthogonal approaches for the comprehensive characterization of structural variants at nucleotide resolution and support the potential utility of long-read sequencing in the molecular diagnostic assessment of BRCA -related CNVs.