Copy Number Profiling of Tumor Samples

SNP array was performed on the 123 samples. Tumor DNA was extracted using the Nucleospin Tissue Kit (Macherey Nagel) and quantified using Qubit dsDNA BR Assay Kit (Life Technologies). Tumor DNA was hybridized with Infinium CytoSNP-850 K Illumina Beadchips (Illumina) according to the manufacturer’s instructions. SNP arrays were scanned on an iScan (Illumina) and data were processed using the genotyping module in Genome Studio v2011.1 (Illumina) to calculate B-allele frequencies (BAF) and logR ratios. GAP method was used to call SCNA and to determine the number of chrs and the ploidy pattern (near-diploid, near-tetraploid) for each tumor [35 (link)]. The GAP method relies on two parameters to estimate tumor ploidy: 1) the DNA index for a tumor genome estimated as an average copy number in a genome divided by 2, and 2) the chromosome counts in a tumor genome estimated as a sum of copy numbers at pericentric regions of each chromosome arm. The calling of SCNA was based on the analysis of logR and allelic ratios [36 (link)]. The purity of the samples was assessed using BAF values. SNP array data are deposited in public repository ArrayExpress under the accession number E-MTAB-6371.