Illumina HumanOmni2.5-8 arrays were used to assay 112 samples (including 105 tumor-normal pairs) for geno-type, DNA copy number and loss of heterozygosity (LOH) at ~2.5 million SNP positions. The data from these arrays were processed as described recently90 (link). The PICNIC algorithm95 (link) was used to estimate normal contamination, ploidy and chromosomal segments with LOH. After adjusting the raw data for normal contamination, the cghFLasso algorithm96 (link) was used to obtain the final estimation and segmentation of total copy number. A subset of 2,228,703 high-quality SNPs was selected for all analyses.
Genomic regions with recurrent DNA copy gain and loss were identified by computing the frequency of a log2 copy number ratio of >0.45 or <−0.45 for gains and losses, respectively, for each tumor subtype. Given that our algorithm for estimating copy number ratios assumes segmental changes, we applied manual recentering to the chRCC data where we observed many whole- chromosome losses.
Genomic regions with recurrent DNA copy gain and loss were identified by computing the frequency of a log2 copy number ratio of >0.45 or <−0.45 for gains and losses, respectively, for each tumor subtype. Given that our algorithm for estimating copy number ratios assumes segmental changes, we applied manual recentering to the chRCC data where we observed many whole- chromosome losses.
