Profiling Cancer Cell Genome Alterations

Detailed procedure of aCGH hybridization and data analysis have been reported previously [13 (link)]. In brief, genomic DNA from 12 human CCOC cell lines were extracted and profiled on the Agilent 105k Human Genome CGH Microarray according to manufacturer’s instructions. Genomic coordinates for this array are based on the NCBI build 36, March 2006 freeze of the assembled human genome (UCSC hg18), available through the UCSC Genome Browser. Data were subsequently imported into CGH Analytics software (version 3.4.40, Agilent Technologies) for visualization. GISTIC analysis was performed to identify disease related amplification and deletion chromosomal regions.