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Fig. 3 | Acta Neuropathologica Communications

Fig. 3

From: DNA methylation alterations across time and space in paediatric brain tumours

Fig. 3

Methylation subclasses are homogeneous spatially, but site-specific alterations occur. A The methylation subclasses (≥ 0.9 is successfully classified; indicated by dashed line) of the included spatial samples are homogeneous for each patient, when considering the 0.9 threshold. B The subclasses were also stable in a cohort of paired medulloblastoma metastases. The first bar indicates the primary tumour and subsequent bars represent metastases. C Phylogenetic tree based on the top 5000 most variable CpG sites for GU-pBT-88 with a paediatric brain control tissue as reference. The phylogenetic trees demonstrate the evolutionary relationship between samples, and which samples that are the most different from each other. The colour denotes the methylation subclass and its calibrated score is written out in parenthesis. GU-pBT-88 has an indication of multiple subclasses, but not confirmed as the calibrated scores are below 0.9. D Differentially methylated positions (DMPs) were identified within each tumour by pairwise comparison of the intratumour biopsies, where a difference in β-value > 0.3 was considered a DMP. The number of DMPs varied between the tumours, and E there was a trend of more DMPs in medulloblastomas than low-grade gliomas. F The DMPs were significantly enriched in regions that were not associated with a gene and decreased in 1st Exon, Exon boundaries and TSS200 (transcription start site and 200 bp away) regions compared to the distribution of the array (first black bar). * denotes significant p-value < 0.01

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