Supplementary Figure 10: Alternative evolutionary analysis from single-sample cross-sectional data with TRONCO.

We show the data (A) and the fit (B). We run the CAPRI algorithm from TRONCO/ PiCnIc on a feature matrix where an entry is 1 if the driver has CCF above 0 in any of the samples of a patient; here we show only the drivers that occur in at least 7% of the samples in the cohort (n = 99), and the fit is run with all driver that occur in at least 2% of the cohort. CAPRI uses a statistical procedure that scans the patterns of co-occurrence of the input alterations in cross-sectional single-sample tumours, and infers a Suppes-Bayes Causal Network. The graph is annotated with non-parametric bootstrap scores, and with REVOLVER’s edge-specific jackknife scores (Supplementary Notes). NA stands for edges that are never detected across resamples. These predicted associations overlap only partially to the trajectories inferred with REVOLVER, which estimates phylogenetic orderings from each patient. For instance, this model is suggesting a possible transition among PIK3CA and SOX2 which, however, is undetected via phylogenetic analysis of TRACERx CCFs. Conversely, no transitions are estimated for EGFR, while phylogenetic analysis determines two subgroups associated to trajectories initiated by such driver.