Temporal dynamics of somatic mutations. SciClone analysis of variant allele frequencies for case S42 revealed 6 predicted subclones (A). Although cluster 1 (harboring a mutation in RPS15), clusters 2 and 3 (carrying a frame-shift deletion in MGA, a gene previously found disrupted in high-risk CLL)^26,27  remained stable over time; clusters 4 and 6 represent relapse-specific (sub)clones, with the latter harboring a TP53 mutation that affects 25% of tumor cells, whereas cluster 5 was eliminated. In case S17, a single stable population was detected; however, a drastic shift in (sub)clonal populations was also observed (B); clusters 4 and 6 were successfully eliminated by treatment. This is noteworthy because the former harbored the classical 2-bp deletion of NOTCH1 and the recurrent p.K700E SNV in SF3B1. On the other hand, clusters 2, 3, and 5 represent relapse-specific subclones with cluster 2, which was the dominant clone at relapse, harboring a stop-gain mutation in NOTCH1 and an SNV in EGR2. Results for the remaining samples are provided in supplemental Figure 4. (A-B) The mean variant allele frequency of each cluster at both time points (top right) and the fraction of each cluster in comparison with the major cluster (cluster 1; bottom right). (C-E) Variant allele frequencies for FCR relapsing cases with RPS15, EGR2, and NOTCH1 mutations before treatment and at relapse. *Denote 2 unique mutations in the same case (S17).