CLL fractions revealed an intraclonal program of accumulated epigenetic changes linked to the longevity of the cells. (A) Scatter plots for pairwise comparisons of DNA methylation between fractions. Differentially methylated CpGs are highlighted as black (FDR-adjusted P < .05) or red (FDR-adjusted P < .05 and β-value difference ≥10%) dots, based on paired linear models generated with the R/Bioconductor package limma. (B) Venn diagram showing IGHV-specific differential methylation between PF and RF (red dots in panel A). (C) Scatter plot illustrating similar tendencies in U-CLL (x-axis) and M-CLL (y-axis) patients for those differences in DNA methylation β-values primarily identified only in U-CLL between RF and PF (red dots in panel A). Relative distribution of DMCs between PF and RF in relation to CpG islands (D) or across chromatin states identified in the lymphoblastoid cell line GM12878 by ChromHMM (E). Distribution of hypomethylated sites is depicted by downward-pointing triangles, while distribution of hypermethylated sites is depicted by upward-pointing triangles. The y-axis shows fold enrichment for the corresponding DMCs over the frequency of all measured CpGs within the same regions, and the x-axis shows the percent of the indicated DMCs that occur in each annotation feature depicted by different colors. Larger symbol sizes depict P < .01. (F) The rate of methylation aging during the CLL life cycle is displayed as difference in DNAm age (years) between the PF and RF intraclonal fractions. Individual CLL patients are color-coded by IGHV mutation status and ranked by absolute difference in the recently born PF cells.