Extended Data Figure 4. Validation of the subclonal hierarchies in A24 and A34.

Validation strategy as described in Extended Data Figure 2. For A24 and A34, hierarchical clustering of the VAF was performed separately for substitutions (a) and (i) and indels (b) and (j). 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. Additional samples for A24 and A34 are incorporated into the phylogenetic tree (c) and (k). The additional cluster in A24, supported by rearrangements only, is indicated by a light green branch in the tree. Numbers of substitutions in WGS data assigned to each subclone are plotted in (d) and (l). VAFs from WGS and validation data, plotted as scatter plots (e) and (m), are very highly correlated. Number of indels (f) and (n) and rearrangements (g) and (o) present in different subsets of samples are plotted as bar charts. Subclone Colour keys for A24 and A34 (h and p) respectively.