ABSOLUTE models common cancer karyotypes by grouping tumor sets according to similarities in their absolute homologous copy-number profiles (Supplementary Fig. 2). These models are constructed directly from the tumor data in a ‘boot-strapping’ fashion, whereby a subset of tumors with relatively unambiguous profiles (e.g., due to high purity values) is used initialize the models, iteratively allowing more tumors to be called, etc. Previous cytogenetic characterizations of human cancer were used to guide this process 13. These models enable calculation of a karyotype likelihood, for each candidate purity/ploidy solution, reflecting the similarity of the corresponding karyotype to models associated with the specified disease of the input tumor sample (8). Integration of the SCNA-fit and karyotype likelihoods favors robust and unambiguous identification of the correct purity and ploidy values in many tumor samples (Supplementary Fig. 1d,h).The selection of a solution implying a less common karyotype requires greater evidence from the SCNA-fit of the copy profile.
