Abstract 2141: Analysis of DNA copy number changes in ovarian cancer data reveals differences in progressive vs. complete response samples

Abstract

Abstract Data from The Cancer Genome Atlas (TCGA) project, related to Ovarian Cancer was obtained from the TCGA web site. The data comprised a total of 489 samples hybridized on 2-color oligo-arrays with 244K probes per array. Raw log-ratio data representing DNA copy number values relative to a DNA pool of normal samples were used in the analysis. The raw data was processed using Nexus Copy Number version 5 software (BioDiscovery, El Segundo CA) and regions of copy number change were identified using the built-in FASST algorithm with significance threshold of 5.0 E-6. After applying a QC filter to remove hybridizations with excessive noise, 463 samples remained for further analysis. Of these, there were 214 solid tumors and 242 normal samples (either surrounding tissue or blood from same patient). In our analysis we compared copy number differences from samples with Progressive disease (n=29) and those with Complete response to therapy (n=245). Using a Fisher's Exact test and a maximum p-value of 0.05 we identified significant regions of copy number change covering a genome area composed of a total of 1049 genes. Included were regions of significant increase in the number of DNA copy number gains in the for the Complete response samples as compared to Progressive cases. The most significant of these were in the 6p21.1 − 6p12.1 and 5p14.1 − 5p13.3 regions. Other regions include a number of well-know genes related to apoptosis, such as TNF (on 6p21.33) and RHOB (on 2p24.1) that were also significantly gained in Complete response but showed DNA loss in Progressive samples. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2141.