Methylome phenotype of the CIMP-low and CIMP-high subgroups in the NOPHO ALL2008 cohort. (A) Differentially methylated CpGs between CIMP-low and CIMP-high leukemias (n = 192 450K+EPICv.1 array-analyzed samples). β-values from EPICv.1 arrays (n = 128 T-ALL and 743 434 CpGs) were merged with 450K arrays (n = 64 T-ALL, 410 369 CpGs), whereafter 380 829 CpGs remained for differential methylation analysis. Of 380 829 CpGs, 3 CpGs had higher mean β-values in CIMP low and 7627 CpGs had higher mean β-values in CIMP high. (B) CGI distribution of the merged array data, the CIMP panel, and the DM-CpGs. (C) Heat map of the β-values of the 7630 DM-CpGs between CIMP subgroups in 192 T-ALL and 3 reference cells. (D) Gene expression (in VST counts) of the corresponding 1046 unique genes annotated to the DM-CpGs in 108 T-ALL and 3 reference cells. Reference cells in panels C and D are CD34⁺, CD3⁺, and lymph node. VST, variance-stabilizing transformation.