Long-Read Nanopore Sequencing Enhances BRCA1/2 Variant Detection Compared with Ion Torrent Analysis

Accurate detection of BRCA1 and BRCA2 variants is essential for breast cancer diagnosis. However, the large size of these genes poses challenges for comprehensive analysis using short-read sequencing, which is generally limited to coding regions and may miss deep intronic and structural variants. This study evaluated the performance of Oxford Nanopore Technology long-read sequencing (ONT-LRS) for comprehensive BRCA1 and BRCA2 analysis and compared its diagnostic yield with Ion Torrent sequencing. In this retrospective study, DNA samples from 27 individuals with breast cancer were initially analyzed using Ion Torrent sequencing, according to standard clinical workflows. Full BRCA1 and BRCA2 genes were subsequently amplified by long-range PCR and sequenced on R10.4.1 flow cells. Variants identified by ONT-LRS were compared with those detected by Ion Torrent. High concordance was observed between ONT-LRS and Ion Torrent for exonic single-nucleotide variants. Importantly, ONT-LRS identified additional variants not detected by Ion Torrent, including a deep intronic variant predicted to alter splicing and one structural variant. This study suggests that ONT-LRS extends the diagnostic capabilities of short-read sequencing by enabling accurate detection of BRCA1 and BRCA2 deep intronic and structural variants that may otherwise be overlooked, with potential implications for patient management and family counseling.