Calculating Variant Allele Fraction of Structural Variation in Next Generation Sequencing by Maximum Likelihood

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dc.contributor.advisorNakhleh, Luay K.en_US
dc.contributor.committeeMemberKavraki, Lydiaen_US
dc.contributor.committeeMemberJermaine, Chrisen_US
dc.contributor.committeeMemberChen, Kenen_US
dc.creatorFan, Xianen_US
dc.date.accessioned2016-01-15T21:40:40Zen_US
dc.date.available2016-01-15T21:40:40Zen_US
dc.date.created2015-05en_US
dc.date.issued2015-04-23en_US
dc.date.submittedMay 2015en_US
dc.date.updated2016-01-15T21:40:40Zen_US
dc.description.abstractCancer cells are intrinsically heterogeneous. Multiple clones with their unique variants co-exist in tumor tissues. The variants include point mutations and structural variations. Point mutations, or single nucleotide variants are those variants on one base; structural variations are variations involving sequence with length not smaller than 50 bases. Approaches to estimate the number of clones and their respective percentages from point mutations have been recently proposed. However, structural variations, although involving more reads than point mutations, have not been quantitatively studied in characterizing cancer heterogeneity. I describe in this thesis a maximum likelihood approach to estimate variant allele fraction of a putative structural variation, as a step towards the characterization of tumor heterogeneity. A software tool, BreakDown, implemented in Perl realizing this statistical model is publicly available. I studied the performance of BreakDown through both simulated and real data, and found BreakDown outperformed other methods such as THetA in estimating variant allele fractions.en_US
dc.format.mimetypeapplication/pdfen_US
dc.identifier.citationFan, Xian. "Calculating Variant Allele Fraction of Structural Variation in Next Generation Sequencing by Maximum Likelihood." (2015) Master’s Thesis, Rice University. <a href="https://hdl.handle.net/1911/87870">https://hdl.handle.net/1911/87870</a>.en_US
dc.identifier.urihttps://hdl.handle.net/1911/87870en_US
dc.language.isoengen_US
dc.rightsCopyright is held by the author, unless otherwise indicated. Permission to reuse, publish, or reproduce the work beyond the bounds of fair use or other exemptions to copyright law must be obtained from the copyright holder.en_US
dc.subjectTumor Heterogeneityen_US
dc.subjectVariant Allele Fractionen_US
dc.subjectStructural Variationen_US
dc.subjectNext Generation Sequencingen_US
dc.titleCalculating Variant Allele Fraction of Structural Variation in Next Generation Sequencing by Maximum Likelihooden_US
dc.typeThesisen_US
dc.type.materialTexten_US
thesis.degree.departmentComputer Scienceen_US
thesis.degree.disciplineEngineeringen_US
thesis.degree.grantorRice Universityen_US
thesis.degree.levelMastersen_US
thesis.degree.nameMaster of Scienceen_US
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