DNA methylation arrays

Bisulfite conversion of DNA for methylation profiling was performed using the EZ DNA Methylation kit (Zymo Research) on 500 ng genomic DNA from all 27 samples. Conversion efficiency was quantitatively assessed by quantitative PCR (qPCR). The Illumina Infinium MethylationEPIC BeadChips were processed as per manufacturer’s recommendations. The R package ChAMP v2.6.4 (Morris et al., 2014) was used to process and analyze the data. For the copy number analysis, the raw IDAT files were uploaded to the MNP tool (Capper et al., 2018), which directly compares the copy number profile estimated from the probe intensities on the methylation array to the distribution observed across thousands of brain tumors in its database.