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PhISCS-BnB: a fast branch and bound algorithm for the perfect tumor phylogeny reconstruction problem

Sadeqi Azer, E; Rashidi Mehrabadi, F; Malikić, S; Li, XC; Bartok, O; Litchfield, K; Levy, R; ... Sahinalp, SC; + view all (2020) PhISCS-BnB: a fast branch and bound algorithm for the perfect tumor phylogeny reconstruction problem. Bioinformatics , 36 (S1) i169-i176. 10.1093/bioinformatics/btaa464. Green open access

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Abstract

MOTIVATION: Recent advances in single-cell sequencing (SCS) offer an unprecedented insight into tumor emergence and evolution. Principled approaches to tumor phylogeny reconstruction via SCS data are typically based on general computational methods for solving an integer linear program, or a constraint satisfaction program, which, although guaranteeing convergence to the most likely solution, are very slow. Others based on Monte Carlo Markov Chain or alternative heuristics not only offer no such guarantee, but also are not faster in practice. As a result, novel methods that can scale up to handle the size and noise characteristics of emerging SCS data are highly desirable to fully utilize this technology. RESULTS: We introduce PhISCS-BnB (phylogeny inference using SCS via branch and bound), a branch and bound algorithm to compute the most likely perfect phylogeny on an input genotype matrix extracted from an SCS dataset. PhISCS-BnB not only offers an optimality guarantee, but is also 10-100 times faster than the best available methods on simulated tumor SCS data. We also applied PhISCS-BnB on a recently published large melanoma dataset derived from the sublineages of a cell line involving 20 clones with 2367 mutations, which returned the optimal tumor phylogeny in <4 h. The resulting phylogeny agrees with and extends the published results by providing a more detailed picture on the clonal evolution of the tumor. AVAILABILITY AND IMPLEMENTATION: https://github.com/algo-cancer/PhISCS-BnB. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Type: Article
Title: PhISCS-BnB: a fast branch and bound algorithm for the perfect tumor phylogeny reconstruction problem
Location: England
Open access status: An open access version is available from UCL Discovery
DOI: 10.1093/bioinformatics/btaa464
Publisher version: https://doi.org/10.1093/bioinformatics/btaa464
Language: English
Additional information: This version is the author accepted manuscript. For information on re-use, please refer to the publisher's terms and conditions.
UCL classification: UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Cancer Institute
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Cancer Institute > Research Department of Oncology
URI: https://discovery.ucl.ac.uk/id/eprint/10112047
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