Cgh analytics software

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.

Array CGH was performed using Human Genome CGH 44K and 180K microarray kits (Agilent Technologies, Santa Clara, CA, USA). Labeling and hybridization were performed according to the supplier’s protocols. Briefly, 1 µg of purified DNA from 50 (20 healthy and 30 peri-implantitis) patient blood samples and 1 µg of pooled sex-matched reference DNA (Promega, Madison, WI, USA) were double-digested with RsaI and AluI for 2 h at 37 °C. After inactivation of the enzymes at 65 °C for 20 min, each digested sample was labeled by random priming (Genomic DNA Enzymatic Labeling Kit, Agilent Technologies) for 2 h using Cy5-dUTP for sample DNA and Cy3-dUTP for reference DNA. The labeled products were then column-purified (Microcon YM-30 filters, Millipore Corporation, Billerica, MA, USA). After probe denaturation and pre-annealing with Cot-1 DNA, hybridization was performed at 65 °C with rotation for 24 h. At the end of the incubation, the slides were washed and analyzed using an Agilent scanner. Data and graphical analyses were performed using CGH Analytics software (v3.1 Agilent Technologies). All map positions were based on the March 2006 NCBI 36/hg18 genome assembly [25 (link)].