A novel virtual barcode strategy for accurate panel-wide variant calling in circulating tumor DNA.

ABSTRACT: BACKGROUND:Hybrid capture-based next-generation sequencing of DNA has been widely applied in the detection of circulating tumor DNA (ctDNA). Various methods have been proposed for ctDNA detection, but low-allelic-fraction (AF) variants are still a great challenge. In addition, no panel-wide calling algorithm is available, which hiders the full usage of ctDNA based 'liquid biopsy'. Thus, we developed the VBCALAVD (Virtual Barcode-based Calling Algorithm for Low Allelic Variant Detection) in silico to overcome these limitations. RESULTS:Based on the understanding of the nature of ctDNA fragmentation, a novel platform-independent virtual barcode strategy was established to eliminate random sequencing errors by clustering sequencing reads into virtual families. Stereotypical mutant-family-leve

SUBMITTER: Wu L 

PROVIDER: S-EPMC7118954 | biostudies-literature | 2020 Apr

REPOSITORIES: biostudies-literature