Genome-wide signatures of differential DNA methylation in pediatric acute lymphoblastic leukemia

We surveyed the DNA methylation levels of 435,941 CpG sites in samples from 764 children at diagnosis of ALL and from 27 children at relapse. This survey uncovered four characteristic methylation signatures. First, compared with control blood cells, the methylomes of ALL cells shared 9,406 predominantly hypermethylated CpG sites, independent of cytogenetic background. Second, each cytogenetic subtype of ALL displayed a unique set of hyper- and hypomethylated CpG sites. The CpG sites that constituted these two signatures differed in their functional genomic enrichment to regions with marks of active or repressed chromatin. Third, we identified subtype-specific differential methylation in promoter and enhancer regions that were strongly correlated with gene expression. Fourth, a set of 6,612 CpG sites was predominantly hypermethylated in ALL cells at relapse, compared with matched samples at diagnosis. Analysis of relapse-free survival identified CpG sites with subtype-specific differential methylation that divided the patients into different risk groups, depending on their methylation status. The DNA methylation levels of primary pediatric ALL samples taken at diagnosis (n= 764), remission(n=86), first relapse (n=27), second relapse (n=5), fractionated blood cells from healthy blood donors (n=51), and methylation +/- controls (n=11) were analyzed with the Illumina Infinium HumanMethylation 450k BeadChips. One ALL sample was run in duplicate (technical replicate). [UPDATE] 04-26-2024: The raw data and processed data were removed from this dataset due to patient privacy concerns.