Abstract C33: Integrated analysis of sequence variations and copy number in TCGA colon adenocarcinoma data

Abstract

Abstract The Cancer Genome Atlas (TCGA) data is available via the TCGA portal and includes copy number data and whole exome sequencing data. Nexus Copy Number 7 was used to evaluate level-1 approved SNP array data from the colon adenocarcinoma (COAD) data set. All samples were subjected to match-paired analysis to evaluate somatic copy number variation. Samples were subjected to extensive pre-processing, including systematic G/C wave correction, ploidy correction, gender correction and quality control. Corresponding level-3 somatic mutation data was used for an integrated analysis of copy number and sequence variation with the COAD data set. Comprehensive copy number analysis identified frequent (>35%) copy number gains of chr7, chr8q, chr13 and chr20, and losses of chr8p, chr17p, and chr18. GISTIC analysis further identified statistically significant focal changes which included loss of FHIT on chr3. Genes KRAS and BRAF were among the most frequently mutated genes. Integrated analysis identified several regions of copy number change that significantly co-occurred with BRAF mutation. Copy number profiles varied significantly between hypermutable and non-hypermutable samples. Potential chromothriptic events were also observed within the COAD dataset. An approach that can integrate structural and sequence variation among samples will be presented. Citation Format: Andrea O'Hara, Raja Keshavan, Louis Culot, Soheil Shams. Integrated analysis of sequence variations and copy number in TCGA colon adenocarcinoma data. [abstract]. In: Proceedings of the Third AACR International Conference on Frontiers in Basic Cancer Research; Sep 18-22, 2013; National Harbor, MD. Philadelphia (PA): AACR; Cancer Res 2013;73(19 Suppl):Abstract nr C33.