Clonal architecture and evolution as determined by mathematical calculation and analysis of sequential samples by WES from the CLL8 trial.⁶⁶  (A) Temporal directed sequence of acquisition of genomic variants inferred from the observation of driver events found at clonal and subclonal frequency in the same samples. Distinct points of origin restricted to a few events, such as 13q− and +12, with early convergence to 11q− and subsequent divergence in diverse late-occurring driver mutations. (B) Comparison of the cancer cell fractions (CCFs) of the putative driver alterations between baseline and relapse samples showed clonal shifts in 57 of 59 cases, of which 21 showed linear and 36 branched evolution with the latter significantly associated with FCR treatment. Notably, variants inferred as early events by temporal network were stably clonal over time. Late events demonstrated either increasing (i.e., in TP53) or shifting (i.e., in SF3B1, ATM) CCFs, suggesting evolution in relation to therapy (grey = stable, red = increasing, and blue = decreasing allele fraction).