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DNA methylation profiling

AB Annamaria Biczok
FS Felix L. Strübing
JE Julia M. Eder
RE Rupert Egensperger
OS Oliver Schnell
SZ Stefan Zausinger
JN Julia E. Neumann
JH Jochen Herms
JT Joerg-Christian Tonn
MD Mario M. Dorostkar
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DNA methylation profiling was performed on cases from which sufficient DNA could be extracted from the tissue. Methylation profiling was done using 100–250 ng DNA on an Illumina Infinium MethylationEPIC BeadChip array (Illumina, San Diego, CA, USA), using the plate reader feature of an Illumina NextSeq 550. The protocols were according to the manufacturer’s instructions. Raw methylation data were analyzed using the DNA methylation-based brain tumor classifier (v11b4), which also provides data on copy-number alterations and MGMT promoter methylation [9]. T-stochastic neighborhood embedding (t-SNE) was calculated in R. Presumably because of DNA degradation, many older cases tended not to match definitively (score >  = 0.9), but a high score (> = 0.5) with compatible histology was deemed sufficient for a diagnosis. The methylation classes and associated scores are reported in detail in the Additional file 2: Table S1.

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