Figure 2

Beta-value distribution and magnitude of differential methylation. Density plots demonstrate the differences in β-value distribution of the differentially methylated CpGs (DMCs) in the different DMC signatures between the ALL patients and reference samples. In each panel, the distribution of all DMC β-values across all patients and controls is plotted on the left side of each panel and the mean difference in β-value for each CpG is plotted on the right side of the panel. The red lines indicate DMCs with increased DNA methylation in ALL and blue lines indicate DMCs with decreased DNA methylation in the line plots. The scales on the x-axis of the density plots and the y-axis of the line plots range from 0 (no methylation) to 1.0 (100% methylation). (A) The distribution of all β-values in the constitutive DMC signature for the 137 reference samples (black dashed line) and 774 ALL samples (black solid line) (left) and the mean difference in β-values (right). (B-I) The β-value distributions of each of the DMCs in the subtype-specific DMC signatures across the reference samples (n = 137, dashed lines) and the ALL samples by immunophenotypic or cytogenetic subtype (colored lines, left). The mean difference in methylation between the reference panel and each subtype is plotted to the right.