Prediction of relapse-free survival using differentially methylated CpGs (DMCs). (A) Performance of the DMC signatures in ALL subtypes stratified according to treatment groups for predicting relapse-free survival using AUC scoring. The treatment groups are indicated by standard risk (SR), intermediate risk (IR), high risk (HR), and infant. The predictive performance of the DMC signatures with AUC >0.60 was assessed by permuting the data 1,000 times. The permuted P-values are indicated in the bar chart. Plots of the methylation levels across the (B) ERVH-3 and (C) DNMBP genes in patients with the t(12;21)ETV6/RUNX1 translocation treated with the standard risk protocol and (D) the precursor microRNA gene (LOC146880/ENSG00000215769) in patients harboring the t(9;22)BCR/ABL1 translocation. DMCs associated with relapse-free survival (P < 0.05) are highlighted above the heatmaps in (B-D) with black lines connecting the CpG site in the gene with the heatmap. The patients (rows) are clustered based on the CpG sites associated with relapse-free survival. The three distinct methylation profiles in the heatmap are indicated by the color bar to the right. The outcome for individual patients is marked by the inner color bar on the right side of the heatmap with patients in remission in black, relapsed patients in red, late relapsed patients in yellow, patients with events other than disease relapse in blue, and patients censored before 5 years of follow-up time in gray. The average methylation levels in the non-leukemic controls are shown below the heatmap. At the bottom of each panel, Kaplan-Meier curves are color-coded by methylation groups, with blue indicating hypomethylation, yellow indicating intermediate methylation, and red indicating hypermethylation. The Kaplan-Meier curves demonstrate the difference in relapse-free survival of patients with different methylation profiles with the Gray’s test P-value for the difference shown in each panel.