Correlation of cytogenetic changes and tumor-specific differential gene expression in colorectal cancer.

e14598 Background: Studies have consistently reported frequent gross cytogenetic changes in tumor genome in colorectal cancer (CRC) – mainly copy number (CN) loss of 8p, 17p, 18q, and gain of 8q, 9p, 13q, 20p, 20q harboring a large number of genes. In this study we tried to identify the genomic regions which show amplification/ deletion in cytogenetic data (structural change at DNA level) and also correlate to tumor-specific differential gene expression (functional consequences at transcriptome level) in CRC tissue. Methods: We studied a set of consecutive 43 left sided microsatellite stable (MSS) adenocarcinoma cases from a series of 86 CRC patients for which we had DNA from fresh frozen sample and RNA from RNA Later preserved sample available from tumor tissue and corresponding healthy colonic tissue for genome-wide assays. Cytogenomic changes were detected using Illumina Human Cyto12 SNP chip. Gene expression data was obtained from Illumina HT12 v4 chips and mutation by sequencing. Results: Using genom...