Analysis of CTCL subtypes identifies genetic hallmarks of leukemia. (A) Swimmer plot of patients with MF who developed leukemia. (B) Heat map depicting the relative contribution of point mutation signatures in CTCL subgroups. Color bar indicates proportion of SSNVs in each group harboring each signature. *q < 0.05 2-sided Student t test comparing SS and MF followed by the Benjamini, Krieger, and Yekutieli correction. (C) Violin plot displaying number of broad SCNVs per sample in each CTCL subtype. P values indicate 2-sided Student t test MF vs SS or MF vs L-MF. (D-F) Heat map depicting prevalence of chromosome arm-level SCNVs (D) and deletions in putative tumor suppressors (E-F) in each CTCL subgroup. (D-F) Color bars indicate proportion of cases in each group with the indicated alteration. Panels E and F share the same scale. *P_adj. < .05, by Fisher’s exact test comparing leukemic CTCL and MF followed by Bonferroni correction. Shared deletions indicates genes >12.5% deleted in each subgroup; leukemia-specific deletions show significant genes deleted in >30% of leukemic CTCLs and <10% of MFs. (G) Genetic similarities and differences across CTCL subgroups.