Multidimensional characterization of the intermediate cell population in CTCL. (A) Three annotated groups of cells from each single-patient analysis are shown on the UMAP plot resulting from integration of the transcriptomes of 11 patients. DEGs among the 3 groups are presented in a heat map. (B) Bar plot displaying the composition of SSNVs (identified via CellSNP) of the intermediate and CTCL groups of a representative patient. SSNVs found in the normal CD4⁺ T-cell population were considered to be individual-specific normal variants (Normal SNV [Background]). Common SSNVs are those mutations found in both the intermediate and CTCL cell populations. (C) Representative inferred SCNV map (identified via InferCNV). (D) Landscape of inferred SCNVs among 10 patients with CTCL. (E) The composition of SCNVs (identified via InferCNV) of the intermediate and CTCL groups. (F) PHATE plot of a single patient with the SCNV level of each cell highlighted. (G) The significantly different level of SCNVs between the intermediate and CTCL cell groups (unpaired t test, ∼10 000 cells).