We used ABSOLUTE to analyze allelic copy-ratio profiles derived from SNP arrays from 3,155 cancer samples, comprising 2,791 tissue specimens and 364 cancer cell lines. The samples came from two TCGA pilot studies describing glioblastoma (GBM; 192 samples) 21 and ovarian carcinoma (488 samples) 33, as well as 2,445 profiles incorporated from a previous pan-cancer copy-number analysis 35 (Online Methods). A minority of these samples (519 or 16.4%) could not be analyzed because they lacked clearly identifiable SCNAs, either because they were nearly euploid (“non-aberrant”), or were excessively contaminated with normal cells (“insufficient purity”), (Fig. 3a). Although sequencing data for somatic point mutations may have resolved these cases, such data were not available for the majority of samples in this cohort35.
