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

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http://hdl.handle.net/10138/303691

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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: University of Helsinki, Genome-scale Algorithmics research group / Veli Mäkinen
University of Helsinki, Research Programs Unit
University of Helsinki, Genome-scale Algorithmics research group / Veli Mäkinen
University of Helsinki, Department of Computer Science
Date: 2019-03-01
Language: eng
Number of pages: 9
Belongs to series: Bioinformatics
ISSN: 1367-4803
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.
Subject: SOMATIC MUTATION
INFERENCE
CANCER
HETEROGENEITY
EVOLUTION
HISTORY
1182 Biochemistry, cell and molecular biology
318 Medical biotechnology
113 Computer and information sciences
111 Mathematics
112 Statistics and probability
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