MIPUP: minimum perfect unmixed phylogenies for multi-sampled tumors via branchings and ILP.

ABSTRACT:

Motivation

Discovering the evolution of a tumor may help identify driver mutations and provide a more comprehensive view on the history of the tumor. Recent studies have tackled this problem using multiple samples sequenced from a tumor, and due to clinical implications, this has attracted great interest. However, such samples usually mix several distinct tumor subclones, which confounds the discovery of the tumor phylogeny.

Results

We study a natural problem formulation requiring to decompose the tumor samples into several subclones with the objective of forming a minimum perfect phylogeny. We propose an Integer Linear Programming formulation for it, and implement it into a method called MIPUP. We tested the ability of MIPUP and of four popular tools LICHeE, AncesTree, CITU

SUBMITTER: Husic E 

PROVIDER: S-EPMC6394401 | biostudies-literature | 2019 Mar

REPOSITORIES: biostudies-literature