Inferred clonal architecture of RHOA mutations and changes to RHOA mutations or haplotypes over time. IGV pileups from a single patient, PTCL_25, (Figure 4C) at 2 timepoints T1 (A) and T4 (B). The data are interpreted to show evolution from a wild-type gene sequence to one showing 2 mutations via a gene sequence bearing a single mutation as shown in the panels to the right of the read pileups. (C) Inferred phylogenetic tree inferred from IGV read pileups. At T1 the dominant clone bears a single c.73A>G (p.Phe25Leu) (dark green) with a subclone that shows both c.73A>G (p.Phe25Leu) and c.48A>T (pCys16*) (light green). At the later timepoint, T4, the dominant clone bears a single c.50G>T (p.Gly17Val) (blue) with a subclone bearing c.50G>T (p.Gly17Val) and c.73A>G (p.Phe25Leu) (purple). Analysis showed the same RHOA phylogenetic tree for both PTCL_10 and PTCL_25. The branch of the tree to the left shows the inferred predominant clonal arrangement at the early timepoint (T1) whereas the branch to the right shows the clones, which emerge at timepoint, T4. For both cases stacked bar charts show the relative frequencies of RHOA mutations or haplotypes in PTCL_25 (D) and PTCL_10 (E). The empty columns indicate that samples were analyzed at these timepoints but that no mutant RHOA was detected. The phylogenetic tree derived from the haplotype data for PTCL_10 is identical to that of PTCL_25 (Figure 5C).