Extended Data Figure 5. Validation of the subclonal hierarchies in A10 and A29.

Validation strategy as described in Extended Data Figure 2. For A10 and A29, hierarchical clustering of the VAF was performed separately for substitutions (a) and (h) and indels (b) and (i). Heatmaps are annotated as described in Extended Data Figure 2. Indels that could not be assigned to any cluster (if any) are annotated with black. Loci with depth <20X are coloured in light blue. The additional sample (D) for A29 is incorporated into the phylogenetic tree (j). Validation experiment for A10-E, the prostate sample, gave very low coverage (d). Subclones for A29-A and A29-C are annotated in the 2d-DP plot (k). Numbers of substitutions in WGS data assigned to each subclone are plotted in (c) and (l). VAFs from WGS and validation data, plotted as scatter plots (d) and (m), are very highly correlated. Number of indels (e) and (n) and rearrangements (f) and (o) present in different subsets of samples are plotted as bar charts. Subclone Colour keys for A10 and A29 (g and p) respectively.