Reconstruction of clonal trees and tumor composition from multi-sample sequencing data.

ABSTRACT:

Motivation

DNA sequencing of multiple samples from the same tumor provides data to analyze the process of clonal evolution in the population of cells that give rise to a tumor.

Results

We formalize the problem of reconstructing the clonal evolution of a tumor using single-nucleotide mutations as the variant allele frequency (VAF) factorization problem. We derive a combinatorial characterization of the solutions to this problem and show that the problem is NP-complete. We derive an integer linear programming solution to the VAF factorization problem in the case of error-free data and extend this solution to real data with a probabilistic model for errors. The resulting AncesTree algorithm is better able to identify ancestral relationships between individual mutations than exi

SUBMITTER: El-Kebir M 

PROVIDER: S-EPMC4542783 | biostudies-literature | 2015 Jun

REPOSITORIES: biostudies-literature