Parameter, noise, and tree topology effects in tumor phylogeny inference.

ABSTRACT:

Background

Accurate inference of the evolutionary history of a tumor has important implications for understanding and potentially treating the disease. While a number of methods have been proposed to reconstruct the evolutionary history of a tumor from DNA sequencing data, it is not clear how aspects of the sequencing data and tumor itself affect these reconstructions.

Methods

We investigate when and how well these histories can be reconstructed from multi-sample bulk sequencing data when considering only single nucleotide variants (SNVs). Specifically, we examine the space of all possible tumor phylogenies under the infinite sites assumption (ISA) using several approaches for enumerating phylogenies consistent with the sequencing data.

Results

On noisy simulated data

SUBMITTER: Tomlinson K 

PROVIDER: S-EPMC6927103 | biostudies-literature | 2019 Dec

REPOSITORIES: biostudies-literature