Benchmarking long-read structural variant calling tools and combinations for detecting somatic variants in cancer genomes.

ABSTRACT: Cancer genomes have a complicated landscape of mutations, including large-scale rearrangements known as structural variants (SVs). These SVs can disrupt genes or regulatory elements, playing a critical role in cancer development and progression. Despite their importance, accurate identification of somatic structural variants (SVs) remains a significant bottleneck in cancer genomics. Long-read sequencing technologies hold great promise in SV discovery, and there is an increasing number of efforts to develop new tools to detect them. In this study, we employ eight widely used SV callers on paired tumor and matched normal samples from both the NCI-H2009 lung cancer cell line and the COLO829 melanoma cell line, the latter of which has a well-established somatic SV truth set. Following separate

SUBMITTER: Aydin SK 

PROVIDER: S-EPMC11906795 | biostudies-literature | 2025 Mar

REPOSITORIES: biostudies-literature