Clonal architecture and evolution of sequential disease episodes. Individual B.I.1 presented with 3 disease episodes (T1-T3), analyzed with WES and deep sequencing. (A) The scatter plot shows WES somatic VAF measurements for T1 and T3. Variants shown in red were shared by T1 and T3, with further evolution of T3 represented by novel clonal (yellow) and subclonal (green) mutations on the vertical axis. Clonal (purple) and subclonal variants (orange and blue) unique to T1 are represented on the horizontal axis. (B) Histogram showing deep sequencing VAF measurements of 28 variants across T1, T2, and T3. T2 was genetically distinct, with no shared variants observed in T1 or T3. In contrast, T1 and T3 shared multiple clonal mutations, with TET2 (p.R571X) representing the only subclonal variant from T1 that was present in T3 (red arrow). (C) The T1 founding clone was characterized by 7q loss with 8 nonsynonymous mutations including CEBPA (p.N281RfsX38) and SMC3 (p.R381Q). The patient received conventional chemotherapy and stem cells were harvested in CR1 (for future use). T3 occurred 3 years after autologous transplantation of these cells, demonstrating expansion of a latent T1-derived subclone, sharing 10 somatic coding variants and the subclonal TET2 mutation (shown in red). Novel clonal variants in T3 included EZH2 (p.R502Q) with a new subpopulation harboring GATA2 and CSF3R mutations. The intervening tumor, T2, was distinct from T1 and T3, characterized by 11p aUPD and 16 novel nonsynonymous variants including the WT1 mutation, p.D223-S233dup. The percentage of cells in each tumor subpopulation is shown relative to the dominant tumor clone.