Meltos: multi-sample tumor phylogeny reconstruction for structural variants.

ABSTRACT:

Motivation

We propose Meltos, a novel computational framework to address the challenging problem of building tumor phylogeny trees using somatic structural variants (SVs) among multiple samples. Meltos leverages the tumor phylogeny tree built on somatic single nucleotide variants (SNVs) to identify high confidence SVs and produce a comprehensive tumor lineage tree, using a novel optimization formulation. While we do not assume the evolutionary progression of SVs is necessarily the same as SNVs, we show that a tumor phylogeny tree using high-quality somatic SNVs can act as a guide for calling and assigning somatic SVs on a tree. Meltos utilizes multiple genomic read signals for potential SV breakpoints in whole genome sequencing data and proposes a probabilistic formulation for esti

SUBMITTER: Ricketts C 

PROVIDER: S-EPMC8215921 | biostudies-literature | 2020 Feb

REPOSITORIES: biostudies-literature