SvCapture: efficient and specific detection of very low frequency structural variant junctions by error-minimized capture sequencing.

ABSTRACT: Error-corrected sequencing of genomic targets enriched by probe-based capture has become a standard approach for detecting single-nucleotide variants (SNVs) and small insertion/deletions (indels) present at very low variant allele frequencies. Less attention has been given to comparable strategies for rare structural variant (SV) junctions, where different error mechanisms must be addressed. Working from samples with known SV properties, we demonstrate that duplex sequencing (DuplexSeq), which demands confirmation of variants on both strands of a source DNA molecule, eliminates false SV junctions arising from chimeric PCR. DuplexSeq could not address frequent intermolecular ligation artifacts that arise during Y-adapter addition prior to strand denaturation without requiring multiple sourc

SUBMITTER: Wilson TE 

PROVIDER: S-EPMC10167630 | biostudies-literature | 2023 Jun

REPOSITORIES: biostudies-literature