Comprehensive Genomic Profiling Pipeline

DNA was hybridized onto Affymetrix SNP 6.0 arrays and normalized as previously described^{6 (link)}. Segmentation was performed using Circular Binary Segmentation algorithm⁵⁶ followed by Ziggurat Deconstruction to infer the length and amplitude each segment. Recurrent focal SCNA peaks were identified using GISTIC2.0⁵⁷ . A peak was considered focally amplified or deleted within a tumor if the GISTIC2.0-estimated focal copy number ratio was greater than 0.1 or less than −0.1, respectively. Purity and ploidy were estimated using ABSOLUTE⁵⁴ . Two peaks were considered the same across tumor types if 1) the known target gene of each peak was the same or 2) the genomic location of the peaks overlapped +/− 1 Mb and each of the overlapping peaks had less than 25 genes and was smaller than 10 Mb.