Serial sample analysis reveals dynamics of resistant clone evolution. Graphical representations (“fish plots”) of clonal evolution shaped by chemotherapy based on ultra-deep sequencing in patients SJALL040461 (A), SJALL018372 (B), and SJALL040462 (C). Treatment history is shown at the top, with drug treatment periods indicated by colors. 6-MP, 6-mercaptopurine; 6-TG, 6-thioguanine. MTX was given weekly during maintenance and is only shown at the beginning of a regimen during maintenance. Clonal evolution is shown in the middle with the vertical axis representing proportion of cells; normal cells are represented by white space. ALL clones are indicated in colors by representative mutations listed below. The minimum tumor purity values (thin line) indicate no detectable ALL cells by ultra-deep sequencing, and their clonal compositions at these times are inferred. Days from diagnosis are indicated at the bottom, with tick marks indicating time points at which samples were sequenced. Samples sequenced by WGS are indicated by black text and tick marks on x-axes, whereas samples with targeted deep sequencing only are shown in gray. In panels B and C, multiple independent CDKN2A deletions are indicated by CDKN2A SV #1, SV #2, and so forth. Variants with alternative possible clonal parentage are indicated by blue asterisks (B). In panel B, the VAF of NT5C2 D407 > DRD at day 322 is 0.007%, but it is shown as larger to enable visualization. In panel C, the surviving clones at days 108 and after are descended from the KMD4B (gray) clone; the KDM4B descendant PCDHGA7 (light-blue) clone and its descendants are dominant at day 356.