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dc.contributor.authorYuan, Xiguoen_US
dc.contributor.authorYu, Guoqiangen_US
dc.contributor.authorHou, Xuchuen_US
dc.contributor.authorShih, Ie-Mingen_US
dc.contributor.authorClarke, Roberten_US
dc.contributor.authorZhang, Junyingen_US
dc.contributor.authorHoffman, Eric Pen_US
dc.contributor.authorWang, Roger Ren_US
dc.contributor.authorZhang, Zhenen_US
dc.contributor.authorWang, Yueen_US
dc.date.accessioned2012-08-29T07:53:32Z
dc.date.available2012-08-29T07:53:32Z
dc.date.issued2012-07-27
dc.identifier.citationBMC Genomics. 2012 Jul 27;13(1):342en_US
dc.identifier.urihttp://hdl.handle.net/10919/18991
dc.description.abstractBackground Somatic Copy Number Alterations (CNAs) in human genomes are present in almost all human cancers. Systematic efforts to characterize such structural variants must effectively distinguish significant consensus events from random background aberrations. Here we introduce Significant Aberration in Cancer (SAIC), a new method for characterizing and assessing the statistical significance of recurrent CNA units. Three main features of SAIC include: (1) exploiting the intrinsic correlation among consecutive probes to assign a score to each CNA unit instead of single probes; (2) performing permutations on CNA units that preserve correlations inherent in the copy number data; and (3) iteratively detecting Significant Copy Number Aberrations (SCAs) and estimating an unbiased null distribution by applying an SCA-exclusive permutation scheme. Results We test and compare the performance of SAIC against four peer methods (GISTIC, STAC, KC-SMART, CMDS) on a large number of simulation datasets. Experimental results show that SAIC outperforms peer methods in terms of larger area under the Receiver Operating Characteristics curve and increased detection power. We then apply SAIC to analyze structural genomic aberrations acquired in four real cancer genome-wide copy number data sets (ovarian cancer, metastatic prostate cancer, lung adenocarcinoma, glioblastoma). When compared with previously reported results, SAIC successfully identifies most SCAs known to be of biological significance and associated with oncogenes (e.g., KRAS, CCNE1, and MYC) or tumor suppressor genes (e.g., CDKN2A/B). Furthermore, SAIC identifies a number of novel SCAs in these copy number data that encompass tumor related genes and may warrant further studies. Conclusions Supported by a well-grounded theoretical framework, SAIC has been developed and used to identify SCAs in various cancer copy number data sets, providing useful information to study the landscape of cancer genomes. Open-source and platform-independent SAIC software is implemented using C++, together with R scripts for data formatting and Perl scripts for user interfacing, and it is easy to install and efficient to use. The source code and documentation are freely available at http://www.cbil.ece.vt.edu/software.htm.en_US
dc.format.mimetypeapplication/pdf
dc.language.isoen_US
dc.rightsCreative Commons Attribution 4.0 International*
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/*
dc.titleGenome-wide identification of significant aberrations in cancer genomeen_US
dc.typeArticle - Refereed
dc.date.updated2012-08-29T07:53:32Z
dc.description.versionPeer Reviewed
dc.rights.holderXiguo Yuan et al.; licensee BioMed Central Ltd.en_US
dc.title.serialBMC Genomics
dc.identifier.doihttps://doi.org/10.1186/1471-2164-13-342
dc.type.dcmitypeText


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Creative Commons Attribution 4.0 International
License: Creative Commons Attribution 4.0 International