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

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Husic , E , Li , X , Hujdurovic , A , Mehine , M , Rizzi , R , Mäkinen , V , Milanic , M & Tomescu , A I 2019 , ' MIPUP : minimum perfect unmixed phylogenies for multi-sampled tumors via branchings and ILP ' , Bioinformatics , vol. 35 , no. 5 , pp. 769-777 . https://doi.org/10.1093/bioinformatics/bty683

Title: MIPUP : minimum perfect unmixed phylogenies for multi-sampled tumors via branchings and ILP
Author: Husic, Edin; Li, Xinyue; Hujdurovic, Ademir; Mehine, Miika; Rizzi, Romeo; Mäkinen, Veli; Milanic, Martin; Tomescu, Alexandru I.
Contributor organization: Genome-scale Algorithmics research group / Veli Mäkinen
Helsinki Institute for Information Technology
Research Programs Unit
Genome-Scale Biology (GSB) Research Program
Department of Medical and Clinical Genetics
Faculty of Medicine
Department of Computer Science
Algorithmic Bioinformatics
Date: 2019-03-01
Language: eng
Number of pages: 9
Belongs to series: Bioinformatics
ISSN: 1367-4803
DOI: https://doi.org/10.1093/bioinformatics/bty683
URI: http://hdl.handle.net/10138/303691
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, CITUP, Treeomics to reconstruct the tumor phylogeny. On simulated data, MIPUP shows up to a 34% improvement under the ancestor-descendant relations metric. On four real datasets, MIPUP's reconstructions proved to be generally more faithful than those of LICHeE.
1182 Biochemistry, cell and molecular biology
318 Medical biotechnology
113 Computer and information sciences
111 Mathematics
112 Statistics and probability
Peer reviewed: Yes
Rights: cc_by
Usage restriction: openAccess
Self-archived version: publishedVersion

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