Distinct leukemia subtypes can be defined based exclusively on their expression profiles. Expression profiles were obtained on leukemic blasts from 132 diagnostic bone marrow aspirates and the data analyzed using (A) an unsupervised 2-dimensional clustering algorithm and (B-D) principle component analysis (PCA). In this analysis the cases in the training and test sets were combined, and the analysis was performed with the 26 825 genes from the Affymetrix U133A and B microarrays that varied in their expression across this dataset. (A) A 2-dimensional hierarchic clustering was performed using Pearson correlation coefficient and unweighted pair group method using arithmetic averages. (B) Multidimensional scaling plot of all cases using PCA. (C) Multidimensional scaling plot of B-lineage ALL cases (n = 118). (D) The identical multidimensional scaling plot as shown in panel C except the plot was rotated 90°. Each case is represented by a sphere and is color coded to indicate the genetic subgroup to which it belongs: BCR-ABL (orange), E2A-PBX1 (aqua), hyperdiploid with more than 50 chromosomes (yellow), MLL (purple), T-ALL (red), TEL-AML1 (green), novel cases (blue), and unclassified cases (gray).