Analysis of gene copy number changes in tumor phylogenetics

dc.contributor.authorZhou, Jun
dc.contributor.authorLin, Yu
dc.contributor.authorRajan, Vaibhav
dc.contributor.authorHoskins, William
dc.contributor.authorFeng, Bing
dc.contributor.authorTang, Jijun
dc.date.accessioned2018-09-03T02:31:59Z
dc.date.available2018-09-03T02:31:59Z
dc.date.issued2016-09-22
dc.description.abstractBACKGOUND Evolution of cancer cells is characterized by large scale and rapid changes in the chromosomal  landscape. The fluorescence in situ hybridization (FISH) technique provides a way to measure the copy numbers of preselected genes in a group of cells and has been found to be a reliable source of data to model the evolution of tumor cells. Chowdhury et al. (Bioinformatics 29(13):189-98, 23; PLoS Comput Biol 10(7):1003740, 24) recently develop a computational model for tumor progression driven by gains and losses in cell count patterns obtained by FISH probes. Their model aims to find the rectilinear Steiner minimum tree (RSMT) (Chowdhury et al. in Bioinformatics 29(13):189-98, 23) and the duplication Steiner minimum tree (DSMT) (Chowdhury et al. in PLoS Comput Biol 10(7):1003740, 24) that describe the progression of FISH cell count patterns over its branches in a parsimonious manner. Both the RSMT and DSMT problems are NP-hard and heuristics are required to solve the problems efficiently. METHODS In this paper we propose two approaches to solve the RSMT problem, one inspired by iterative methods to address the "small phylogeny" problem (Sankoff et al. in J Mol Evol 7(2):133-49, 27; Blanchette et al. in Genome Inform 8:25-34, 28), and the other based on maximum parsimony phylogeny inference. We further show how to extend these heuristics to obtain solutions to the DSMT problem, that models large scale duplication events. RESULTS Experimental results from both simulated and real tumor data show that our methods outperform previous heuristics (Chowdhury et al. in Bioinformatics 29(13):189-98, 23; Chowdhury et al. in PLoS Comput Biol 10(7):1003740, 24) in obtaining solutions to both RSMT and DSMT problems. CONCLUSION The methods introduced here are able to provide more parsimony phylogenies compared to earlier ones which are consider better choices.en_AU
dc.description.sponsorshipJZ, WH, BF and JT were funded by NSF IIS 1161586 and an internal grant from Tianjin University, China.en_AU
dc.format11 pagesen_AU
dc.format.mimetypeapplication/pdfen_AU
dc.identifier.urihttp://hdl.handle.net/1885/147055
dc.publisherBioMed Centralen_AU
dc.rights© 2016 The Author(s). This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/ publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.en_AU
dc.sourceAlgorithms for molecular biology : AMBen_AU
dc.subjectchromosomal duplicationen_AU
dc.subjectfishen_AU
dc.subjectgene copy numberen_AU
dc.subjectgene duplicationen_AU
dc.subjectmaximum parsimonyen_AU
dc.subjectrectilinear steiner minimum treeen_AU
dc.subjecttumor phylogenyen_AU
dc.subjectwhole genome duplicationen_AU
dc.titleAnalysis of gene copy number changes in tumor phylogeneticsen_AU
dc.typeJournal articleen_AU
dcterms.accessRightsOpen Accessen_AU
dcterms.dateAccepted2016-09-08
local.bibliographicCitation.issue1en_AU
local.bibliographicCitation.startpage26en_AU
local.contributor.affiliationLin, Yu, Research School of Computer Science, College of Engineering and Computer Science, The Australian National Universityen_AU
local.contributor.authoremailyu.lin@anu.eduen_AU
local.contributor.authoruidu1024708en_AU
local.identifier.ariespublicationa383154xPUB6793
local.identifier.citationvolume11en_AU
local.identifier.doi10.1186/s13015-016-0088-2en_AU
local.identifier.essn1748-7188en_AU
local.identifier.scopusID2-s2.0-84995622029
local.identifier.thomsonID000388899700001
local.identifier.uidSubmittedByu4579722en_AU
local.publisher.urlhttps://www.biomedcentral.com/en_AU
local.type.statusPublished Versionen_AU

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