Underlying differences in DNA methylation distinguish MDS from de novo AML. (A-C) Unsupervised clustering analysis of 14 MDS cases and 15 de novo AML samples with 3 different methods: COA, PCA, and hierarchical clustering. (D) Plot of DNA methylation difference between MDS and de novo AML cases (x-axis) versus statistical significance (y-axis). Red points mark probe sets that reached both criteria for differential methylation on our analysis [P < .0005 and absolute fold change in log(HpaII/MspI) > 1.5], whereas blue points mark probe sets that reached statistical significance but did not have a change in log(HpaII/MspI) greater than 1.5. (E) Two-dimensional hierarchical clustering of genes differentially methylated between MDS and de novo identified by supervised analysis, illustrated with a heatmap. Cases are represented in the columns and probe sets in the rows. (F) Three-dimensional representation of PCA analysis, including normal CD34⁺ cells, de novo AML, and MDS. MDS samples can all be found the furthest away from normal CD34 cells, whereas de novo AML tend to cluster in an intermediate position between the other 2 groups of samples.