Figure 2.

Gene expression and immunophenotypic features of ETP-ALL. (a) Unsupervised clustering analysis of diagnostic bone marrow samples from 55 pediatric patients with T-ALL, using a set of genes differentially expressed in ETP (Supplementary Table 1).¹¹;¹⁴–¹⁶ One cluster (indicated by red bars) had a gene expression profile resembling that of ETP cells. (b) Flow cytometric contour dot plots illustrating the immunophenotypes of normal thymocytes (discarded material from infants undergoing open heart surgery), and representative cases of ETP and typical T-ALL. Each sample was labeled simultaneously with the indicated antibodies (cCD3 = cytoplasmic CD3) and analyzed with an LSRII flow cytometer and DIVA software using a log density and biexponential setting. Vertical and horizontal lines in each plot correspond to zero immunofluorescence. (c) The heat map shows percentages of positive leukemic cells for each of the listed markers among the 139 St Jude T-ALL cases studied at diagnosis; gray indicates missing data. Each row represents one case and each column the percentage of positive leukemic cells with the indicated marker. (d) Heat map of the top 150 differentially expressed genes (see Supplementary Table 3), ranked by P value.