Fig. 2

Differentially methylated CpG sites in pilocytic and diffuse astrocytomas: comparison with normal brain tissue, and characteristics. a Hierarchical clustering of pilocytic and diffuse astrocytomas, normal controls, and additional brain samples. Test tumours: PA, pilocytic astrocytomas; DA, diffuse astrocytomas. Controls: FFL, Foetal frontal lobe; FB, foetal brain; FCB, foetal cerebellum; AB, adult brain, ACB, adult cerebellum; NSC, neural stem cells. Additional datasets from normal brain tissue are derived from GEO Accession GSE41826: 4782 N/4782G, 165 N/165G, 1230 N/1230G, 1497 N/1497G, neuronal or glial component of cerebral cortex; MIX1 and MIX7, mix of glial and neuronal components of cerebral cortex [12]. The overwhelming majority of hypomethylated sites are specific to pilocytic astrocytomas. Two main branches emerge, one of which contains most of the pilocytic astrocytomas and the other contains the normal brain controls and diffuse astrocytomas, which grouped with glial component of the cerebral cortex. Foetal brain regions and adult cerebellum clustered together. A subset of astrocytomas grouped with the neural stem cells. Columns represent individual samples; rows represent 450K CpG probes. As four values were missing in the normal brain dataset only 311/315 sites are shown. Methylation beta values are represented in shades of yellow = 0 (unmethylated) to blue = 1 (methylated). b Validation of the hypomethylated signature in a larger published set of pilocytic astrocytomas (PA validation set 2; n = 61; GSE44684 [27]). The hypomethylation signature was identified in both infratentorial and supratentorial pilocytic astrocytomas. BRAF-fusions were present in 51/62 samples in this tumour set. Only 287/315 sites were present in the published data set. Tumour samples on the left of the red line are the test tumours in the current study, samples on the right of the line are validation set. Columns represent individual samples; rows 450K CpG probes. c Distribution of the 315 differentially methylated CpG sites across the Illumina 450K-annotated location CpG features. TSS1500, 201-1500 bp upstream of transcription start (TSS); TSS200, up to 200 bp upstream of the TSS; UTR, untranslated region d Distribution of the 315 differentially methylated sites in regions of high, intermediate and low CpG density [42]. HC, high CpG density; IC, intermediate CpG density; IC shore, intermediate CpG density shore; LC, low CpG density