Towards accurate characterization of clonal heterogeneity based on structural variation

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dc.citation.firstpage299en_US
dc.citation.journalTitleBMC Bioinformaticsen_US
dc.citation.volumeNumber15en_US
dc.contributor.authorFan, Xianen_US
dc.contributor.authorZhou, Wandingen_US
dc.contributor.authorChong, Zechenen_US
dc.contributor.authorNakhleh, Luayen_US
dc.contributor.authorChen, Kenen_US
dc.date.accessioned2014-10-30T19:33:32Zen_US
dc.date.available2014-10-30T19:33:32Zen_US
dc.date.issued2014en_US
dc.description.abstractRecent advances in deep digital sequencing have unveiled an unprecedented degree of clonal heterogeneity within a single tumor DNA sample. Resolving such heterogeneity depends on accurate estimation of fractions of alleles that harbor somatic mutations. Unlike substitutions or small indels, structural variants such as deletions, duplications, inversions and translocations involve segments of DNAs and are potentially more accurate for allele fraction estimations. However, no systematic method exists that can support such analysis. In this paper, we present a novel maximum-likelihood method that estimates allele fractions of structural variants integratively from various forms of alignment signals. We develop a tool, BreakDown, to estimate the allele fractions of most structural variants including medium size (from 1 kilobase to 1 megabase) deletions and duplications, and balanced inversions and translocations. Evaluation based on both simulated and real data indicates that our method systematically enables structural variants for clonal heterogeneity analysis and can greatly enhance the characterization of genomically instable tumors.en_US
dc.identifier.citationFan, Xian, Zhou, Wanding, Chong, Zechen, et al.. "Towards accurate characterization of clonal heterogeneity based on structural variation." <i>BMC Bioinformatics,</i> 15, (2014) BioMed Central: 299. http://dx.doi.org/10.1186/1471-2105-15-299.en_US
dc.identifier.doihttp://dx.doi.org/10.1186/1471-2105-15-299en_US
dc.identifier.urihttps://hdl.handle.net/1911/77673en_US
dc.language.isoengen_US
dc.publisherBioMed Centralen_US
dc.rightsThis article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. 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_US
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/en_US
dc.subject.keywordstructural variationen_US
dc.subject.keywordclonal heterogeneityen_US
dc.subject.keywordvariant allele fractionen_US
dc.titleTowards accurate characterization of clonal heterogeneity based on structural variationen_US
dc.typeJournal articleen_US
dc.type.dcmiTexten_US
dc.type.publicationpublisher versionen_US
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