Closing the gaps, and improving somatic structural variant analysis and benchmarking using CHM13-T2T.

ABSTRACT: The complexities of cancer genomes are becoming more easily interpreted due to advancements in sequencing technologies and improved bioinformatic analysis. Structural variants (SVs) represent an important subset of somatic events in tumors. While the detection of SVs has been markedly improved by the development of long-read sequencing, somatic variant identification and annotation remain challenging. We hypothesized that the use of a completed human reference genome (CHM13-T2T) would improve somatic SV calling. Our findings in a tumor-normal matched benchmark sample and three patient samples show that the CHM13-T2T improves SV detection accuracy compared to GRCh38 with a notable reduction in false-positive calls, and thus supports improved prioritization. We also overcame the lack of anno

SUBMITTER: Paulin LF 

PROVIDER: S-EPMC12047239 | biostudies-literature | 2025 Apr

REPOSITORIES: biostudies-literature