CN and expression analysis in molecular subgroups of PTCL. (A) Frequency of chromosomal gains and losses found in PTCL-GATA3 and PTCL-TBX21 tumors. Candidate genes in focal regions are indicated. (B). The relative mRNA expression (n = 157, previously molecularly classified PTCL-NOS7,8 ) and median-centered log2 mRNA expression (n = 47, CN cases with Affymetrix HG-U133 Plus2 gene expression data) of select recurrently aberrant genes with differential gene expression relative to DNA CN status. In the relative mRNA expression plots (left panel), colored bars (except gray) indicate cases included in the present CN analysis. Kaplan-Meier curves comparing specific gene aberrations in the PTCL-NOS entity, PTCL-GATA3 subgroup, and combined with a previously published PTCL-NOS series23 are included for CDKN2A, which tended to be associated with poor OS. (C) Validation of genes within recurrent loci observed in the PTCL-GATA3 subgroup using the NanoString Cancer CNV assay. (D) Kaplan-Meier curves comparing the upper vs lower halves of CDKN2A mRNA expression from all molecular PTCL-NOS cases with GEP and outcome data (n = 125) from (B) (left panel) and only in PTCL-GATA3 (n = 52; right panel). (E) Frequency plots of chr6 and chr14 alterations, which have differential regions of abnormality in PTCL-GATA3 and PTCL-TBX21 subgroups. Candidate target genes within the regions are noted.