Summary of experimental methods and data analysis. (A) From 31 patients with MF, 49 biopsies were obtained. In 6 patients with tumor (TMR) stage disease, paired biopsies from TMRs and late-stage plaques (LSPs) were obtained. (B) TMR cell clusters microdissected from the lesional skin and matching control tissue (peripheral blood or the epidermis; not shown) were sequenced by whole-exome sequencing (WES). (C) The genetic aberration data (single-nucleotide variants [SNVs] and CNAs) were used for the reconstruction of MF phylogenetic trees. CNA, copy-number aberration; ESP, early-stage plaque; GATK, Genome Analysis Toolkit; PCR, polymerase chain reaction; SSV, single-somatic variants; TCF, tumor cell fraction; WGS, whole-genome sequencing.