Identified amplification regions by high-density array CGH in a human colorectal adenocarcinoma cell line NCI-H716 [custom 180K]

Double minutes (DMs), a major form of gene amplification, commonly carry oncogenes or chemoresistance-related genes that are associated with the occurrence, development and prognosis of tumors. Thus, probing molecular structures of DMs allows us to further understand molecular mechanisms underlying tumorigenesis. In this study, we identified four amplification regions by high-density array CGH in a human colorectal adenocarcinoma cell line NCI-H716. These amplification regions localized in two populations of DMs. Through a combined analysis on the results of array CGH, high throughput sequencing, multiplex-fluorescence in situ hybridization and chromosome walking results, we constructed molecular structures of the two populations of DMs at nucleotide resolution. Oligonucleotide-based Human Genome Microarrays (Agilent Technologies) containing 60K, 180K, 400K and 1M features were used for hybridization, among which 2×400K format was used to examine genome-wide copy number alteration in a human colorectal adenocarcinoma cell line NCI-H716. The 4×180K format targeting amplified regions was customized microarray that we created by using the Agilent eArray online system (https://earray.chem.agilent.com/‎) for interrogating the genome of DMs with high-resolution and accuracy.