Fig. 3

Evolutionary history of tumor subclones from patient A31. a SNV-based phylogeny. Reproduction of the SNV-based phylogeny as described in Gundem et al. [40] for the multi-sample prostate cancer tumor case with one sample (C) from the primary tumor and four samples (A, D, E, and F) from distinct metastatic sites. Original reconstruction was performed using an n-dimensional Bayesian Dirichlet process to cluster estimated cancer cell fractions of the single-nucleotide variants (SNV) identified in the WGS across samples. Only the major subclone of each sample is shown (“Methods”). b MEDICC2 phylogeny. Using multi-sample phased copy-number profiles, MEDICC2 detected the presence of WGD in the metastatic samples and its absence in the primary sample from A31. The MEDICC2 analysis identifies multiple MSAI events as well as parallel LOH on 6 and 13 (purple arrows). Individual events are marked in the copy-number track where they occur: gains (red) and losses (blue). The gray number in each branch corresponds to its bootstrap-confidence score while the WGD events from the MEDICC2 event detection are marked in green