Fig. 1

Distribution of 5-hmC in tumor samples and median beta values by tumor class and cytosine modifications in CNS tumors as compared to non-tumor brain tissue. a Consistent with studies in other tumor types, 5-hydroxymethylation levels are depleted compared to non-tumor samples; this depletion holds across tumor types. Two-tailed Welch’s t test comparing median values was performed and differences met statistical significance. b Total methylation levels do not differ significantly between tumor and non-tumor samples. c Examined the empirical cumulative distribution of median 5-hydroxymethylcytosine and 5-methylcytosine across 27 primary pediatric central nervous system tumors. While 5mC demonstrates a bimodal distribution, 5hmC is far more sparsely distributed. d Cumulative proportions of Spearman correlation coefficients calculated for each CpG across all tumors. e Ordered distribution of CpG-specific median 5hmC values across the EPIC array in tumor samples. The x axis represents percentile rank of CpG by median beta value. We isolated CpGs with medians greater than the 95th percentile and called these high 5hmC CpGs. This corresponded to 37, 173 loci with a median beta value greater than 0.09. We based subsequent analyses on these high 5hmC CpGs