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dc.contributor.authorHou, Xuchuen
dc.date.accessioned2013-02-19T22:39:36Zen
dc.date.available2013-02-19T22:39:36Zen
dc.date.issued2013-01-07en
dc.identifier.othervt_gsexam:207en
dc.identifier.urihttp://hdl.handle.net/10919/19235en
dc.description.abstractSomatic Copy Number Alterations (CNAs) are common events in human cancers. Identifying CNAs and Significant Copy number Aberrations (SCAs) in cancer genomes is a critical task in searching for cancer-associated genes. Advanced genome profiling technologies, such as SNP array technology, facilitate copy number study at a genome-wide scale with high resolution. However, due to normal tissue contamination, the observed intensity signals are actually the mixture of copy number signals contributed from both tumor and normal cells. This genetic confounding factor would significantly affect the subsequent copy number analyses.
In order to accurately identify significant aberrations in contaminated cancer genome, we develop a Java AISAIC package (Accurate Identification of Significant Aberrations in Cancer) that incorporates recent novel algorithms in the literature, BACOM (Bayesian Analysis of Copy number Mixtures) and SAIC (Significant Aberrations in Cancer). Specifically, BACOM is used to estimate the normal tissue contamination fraction and recover the "true" copy number profiles. And SAIC is used to detect SCAs using large recovered tumor samples. Considering the popularity of modern multi-core computers and clusters, we adopt concurrent computing using Java Fork/Join API to speed up the analysis.
We evaluate the performance of the AISAIC package in both empirical family-wise type I error rate and detection power on a large number of simulation data, and get promising results. Finally, we use AISAIC to analyze real cancer data from TCGA portal and detect many SCAs that not only cover majority of reported cancer-associated genes, but also some novel genome regions that may worth further study.
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dc.format.mediumETDen
dc.publisherVirginia Techen
dc.rightsIn Copyrighten
dc.rights.urihttp://rightsstatements.org/vocab/InC/1.0/en
dc.subjectCopy Number Alterationsen
dc.subjectNormal Tissue Contaminationen
dc.subjectSignificant Copy number Aberrationsen
dc.subjectConcurrent Computingen
dc.titleAccurate Identification of Significant Aberrations in Cancer Genome: Implementation and Applicationsen
dc.typeThesisen
dc.contributor.departmentElectrical and Computer Engineeringen
dc.description.degreeMaster of Scienceen
thesis.degree.nameMaster of Scienceen
thesis.degree.levelmastersen
thesis.degree.grantorVirginia Polytechnic Institute and State Universityen
thesis.degree.disciplineComputer Engineeringen
dc.contributor.committeechairWang, Yue J.en
dc.contributor.committeememberOzcan, Ibrahim Alpayen
dc.contributor.committeememberYu, Guoqiangen


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