Long-read sequencing bridges germline and somatic variant detection: a multi-modal approach for hereditary cancer diagnostics.

BACKGROUND

Effective management of hereditary cancers requires the accurate detection of both germline and somatic pathogenic variants. Conventional approaches, such as liquid biopsy and short-read sequencing, are widely used but may have limitations in resolving structural variants (SVs), providing phasing information, and capturing complex genomic alterations. Oxford Nanopore Technologies (ONT) long-read sequencing enables improved characterization of SVs and phasing, providing additional insights for germline variant analysis.

AIM: In this study, we implemented a multi-modal workflow in 50 cancer patients, integrating plasma-based liquid biopsy, short-read next-generation sequencing (NGS) and ONT-based germline testing.

RESULTS

Somatic mutations were identified in 72% (36/50) of patients, primarily involving TP53, PIK3CA, EGFR, and KRAS. In parallel, germline sequencing revealed pathogenic or likely pathogenic variants in 60% (30/50) of patients, including alterations in BRCA2, MSH2, and CHEK2. Importantly, 10% (5/50) of patients harbored clinically actionable germline variants that were not detected by liquid biopsy, whereas 22% (11/50) showed somatic-only alterations. Notably, 18% (9/50) of patients had no detectable pathogenic variants in either analysis, potentially reflecting biological factors such as low circulating tumor DNA (ctDNA) levels or limitations in panel coverage.

CONCLUSION

These findings highlight the complementary and non-redundant roles of somatic liquid biopsy and germline analyses. Rather than indicating diagnostic equivalence, the results show that each approach captures distinct but clinically relevant genomic information. The inclusion of ONT long-read sequencing may improve the characterization of inherited variants, particularly structural variants and phasing and may support more comprehensive risk assessment and therapeutic planning.