Copy number segmentations were generated by CNVkit78 using default settings (bcbio-nextgen v0.9.3). SCNA breakpoints were defined as the ends of non-diploid segments. Assuming tumor purity of 50%, the estimated mean purity of these tumors, non-diploid segments were defined as segments with log2(tumor coverage/normal coverage) < log2(1.5/2) or log2(tumor coverage/normal coverage) > log2(2.5/2).