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Hujdurovic, Ademir; Kacar, Ursa; Milanic, Martin; Ries, Bernard; Tomescu, Alexandru I.
IEEE/ACM transactions on computational biology and bioinformatics, 2018-Jan.-Feb.-1, 2018 Jan-Feb, 2018-1-1, 20180101, Letnik: 15, Številka: 1Journal Article
Hajirasouliha and Raphael (WABI 2014) proposed a model for deconvoluting mixed tumor samples measured from a collection of high-throughput sequencing reads. This is related to understanding tumor evolution and critical cancer mutations. In short, their formulation asks to split each row of a binary matrix so that the resulting matrix corresponds to a perfect phylogeny and has the minimum number of rows among all matrices with this property. In this paper, we disprove several claims about this problem, including an NP-hardness proof of it. However, we show that the problem is indeed NP-hard, by providing a different proof. We also prove NP-completeness of a variant of this problem proposed in the same paper. On the positive side, we propose an efficient (though not necessarily optimal) heuristic algorithm based on coloring co-comparability graphs, and a polynomial time algorithm for solving the problem optimally on matrix instances in which no column is contained in both columns of a pair of conflicting columns. Implementations of these algorithms are freely available at https://github.com/alexandrutomescu/MixedPerfectPhylogeny.
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in: SICRIS
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