Fig. 1

DNA methylation alterations in the pediatric pan-cancer data. (a) The proportion of differentially methylated CpG sites (DMCs) in nine pediatric cancers (n = 2,016). The proportions of hypermethylated (higher methylation level in tumors than in normal tissues) and hypomethylated (lower methylation level in tumors than in normal tissues) DMCs are separately denoted in different colors. Average proportions of DMCs in pediatric cancers are shown as the orange solid line. AML, Acute myeloid leukemia. B-ALL, B-cell acute lymphoblastic leukemia. ETMR, Embryonal tumors with multilayered rosettes. GBM, Glioblastoma. NBL, Neuroblastoma. PA, Pilocytic astrocytoma. PNET, Primitive neuroectodermal tumor. T-ALL, T-cell acute lymphoblastic leukemia. WT, Wilms tumor. (b) Boxplots illustrating the proportions of hypermethylated and hypomethylated DMCs in pediatric and adult cancers. The proportion is calculated based on all the tested CpGs. (c) The percentage of DMCs that are shared across pediatric and adult cancers is shown in the pie chart for pediatric cancers. There were 15 adult cancers in total (n = 6,391). In Supplementary Tables 1, adult cancers were described in detail. (d) Distribution of overlapped DMCs between pediatric cancers. Regarding overlapped DMCs, a consistent hyper- or hypomethylated state is needed in cancers. (e) A heatmap of methylation changes for shared DMCs (SDMCs) between cancers and normal samples in nine pediatric (n = 2,016) and 15 adult cancers (n = 6,391). Non-significant changes are colored in white. BLCA, Bladder urothelial carcinoma. BRCA, Breast invasive carcinoma. COAD, Colon adenocarcinoma. ESCA, Esophageal carcinoma. HNSC, Head and neck squamous cell carcinoma. KIRC, Kidney renal clear cell carcinoma. KIRP, Kidney renal papillary cell carcinoma. LIHC, Liver hepatocellular carcinoma. LUAD, Lung adenocarcinoma. LUSC, Lung squamous cell carcinoma. PAAD, Pancreatic adenocarcinoma. PRAD, Prostate adenocarcinoma. READ, Rectum adenocarcinoma. THCA, Thyroid carcinoma. UCEC, Uterine corpus endometrial carcinoma. (f) SDMC depletion or enrichment in genomic features compared to 1,000 CpG randomizations. Hypermethylated and hypomethylated SDMCs are separately analyzed and denoted in different colors. (g) Associations between SDMC methylation and gene expression in pediatric tumor samples (n = 238). FDR values were calculated using the Bonferroni method. Since a single gene may produce multiple different mRNAs (i.e., transcripts) that associate with the same SDMC, we only show the best-associated result for each SDMC.