Extended Data Fig. 6: Clonal dynamics from CLL to RT.

a. Subclonal reconstruction and clonal evolution of three cases (3299, 12 and 365) with WGS and scDNA-seq data available. The upper fish plot shows the clonal evolution along the course of the disease inferred from WGS analyses. Each color represents a different subclone and their height is proportional to their cancer cell fraction (CCF) in each time point (vertical lines). The treatments that the patient received and the elapsed time (in years) between samples are indicated at the top. The tissue is indicated for samples of patient 3299 in which different tissues were analyzed by WGS and scDNA-seq in the same time point. The phylogeny of the subclones is depicted together with the main driver alterations (top right). The lower bar plots show the dynamics of the different subclones according to the scDNA-seq analyses. The total number of cells per sample is shown at the bottom. The number of cells assigned to each subclone can be found in Supplementary Table 20. The mutation tree inferred from scDNA-seq data is shown at the bottom-right part. b-c. Subclonal architecture and dynamics of six cases with longitudinal samples (b) and two cases with spatial samples (c) analyzed by WGS.