Pathway-based clonal analysis. (A) For each pathway, we give the mean and 95% credible intervals of the ratio (P1(1 − P2)) / ((1 − P1) P2) (in log₂ scale), where P1 is the probability given the data that the pathway harbors a mutation that clonally expands (ie, its CCF shows a significant increase) in the transition from PB-CLL to tissue-RS. Similarly, P2 is the probability given the data that the pathway harbors a mutation that clonally contracts in the transition to RS. Pathways with FDR < 5%, are highly likely to harbor clonally expanding (rather than contracting) mutations during transformation to RS. (B) Clonal transition events in the gene sets with FDR < 1%, that is, DDR genes and the MAPK-signaling pathway. Each line corresponds to a single SNV or InDel. The color encodes the gene harboring the corresponding mutation (shown at the bottom of the graph).