Integrating SNVs and CNAs on a phylogenetic tree from single-cell DNA sequencing data.

ABSTRACT: Single-cell DNA sequencing enables the construction of evolutionary trees that can reveal how tumors gain mutations and grow. Different whole-genome amplification procedures render genomic materials of different characteristics, often suitable for the detection of either single-nucleotide variation or copy number aberration, but not ideally for both. Consequently, this hinders the inference of a comprehensive phylogenetic tree and limits opportunities to investigate the interplay of SNVs and CNAs. Existing methods such as SCARLET and COMPASS require that the SNVs and CNAs are detected from the same sets of cells, which is technically challenging. Here we present a novel computational tool, SCsnvcna, that places SNVs on a tree inferred from CNA signals, whereas the sets of cells rendering t

SUBMITTER: Zhang L 

PROVIDER: S-EPMC10760445 | biostudies-literature | 2023 Dec

REPOSITORIES: biostudies-literature