Chromosome analysis suite 2.0 chas

Genome-wide DNA copy number and LOH analysis was performed in 13 of 14 cases using the Affymetrix OncoScan FFPE assay (Affymetrix, CA, USA), which utilizes molecular inversion probe technology and is optimized to work on DNA derived from FFPE tissue samples [35 (link)].
Sample preparation, hybridization and scanning were performed according to the manufacturer's specifications. Analysis was performed using the Affymetrix Chromosome Analysis Suite 2.0 (ChAS) and Nexus Copy Number 7.5 software (Biodiscovery, Inc. CA, USA). All copy number alterations and regions of LOH recognized by the software were verified visually to determine erroneous calls and identify clonal or subclonal gains and losses not detected by the software. Analysis was restricted to gains and losses >1 Mb in length (Supplementary Table 4). Genomic alterations were reported based on the NCBI build 37 (hg19) of the human genome and cancer-associated genes were curated from the Cancer Gene Census (COSMIC v61 Release; http://www.sanger.ac.uk/genetics/CGP/Census/)

Genome-wide copy number and LOH analysis was performed for 16 cases using the Affymetrix OncoScan FFPE assay (Affymetrix, CA, USA). Briefly, the Oncoscan assay has been optimized to work with DNA from FFPE tissue, utilizing molecular inversion probes to identify changes in copy number and loss of heterozygosity. [54 (link)] DNA extraction, sample preparation, hybridization, and scanning were performed according to the manufacturer's specifications. Analysis was performed using the Affymetrix Chromosome Analysis Suite 2.0 (ChAS) and Nexus Copy Number 7.5 software (Biodiscovery, Inc. CA, USA).
All copy number alterations and regions of LOH called by the software were verified manually to determine erroneous calls and identify clonal gains and losses undetected by the software(s). Analysis was restricted to gains and losses > 1 Mb in length. Genomic alterations are reported based on the NCBI build 37 (hg19) of the human genome and cancer-associated genes were curated from the Cancer Gene Census (COSMIC v61 Release;http://www.sanger.ac.uk/genetics/CGP/Census/).