Copy number variations (CNVs) identify distinct malignant subclones phylogenetically intermixed between CTCL tissues. (A) Subclonal populations are colored based on inferred CNV analysis . Predicted regions of copy number gain (in red) or loss (in blue) highlighted across the genomic position (columns) and single cells (rows) divided into their subclonal branches from phylogenetic analysis.(B) Plot showing gain (in red) and loss (in blue) events in CNV defined subclones from the skin- and blood-derived clonal malignant T cells from 5 patients (SS1-MF stage IV1) and blood from 2 patients (SS6 and SS7). Skin derived CNV states are shown as dashed lines and blood derived CNV states as solid lines. CNV states with less than 1% frequency in their tissue or based on less than 5 cells were filtered out. (C) Representative phylogram of the malignant skin- and blood-derived T cells of a CTCL patient (SS1) bootstrapped 100 times and rooted using their non-malignant polyclonal T cells to determine malignant evolution of CNV defined clusters. Branch length depicts level of CNV burden. (D) Representative river plot showing connections between GEX based malignant subclusters and CNV defined malignant subclones in a CTCL patient (SS1).