Infinium hd ffpe dna restore kit

DNA methylation and copy number analyses were performed using the Infinium Methylation450k and EPIC BeadChip array platforms (Illumina, USA). All analyses were performed according to the manufacturer’s instructions. In brief, DNA was extracted from FFPE tumor samples using the Maxwell RSC FFPE Plus DNA Purification Kit (Promega, USA). After bisulfite conversion using the Zymo EZ Methylation Kit (Zymo Research Irvine, USA), the Infinium HD FFPE DNA Restore Kit was used for DNA restoration. The beadchips were scanned on the iScan system (Illumina, USA). The unprocessed output data (.idat files) from the iScan reader were checked for general quality measures as indicated by the manufacturer. DNA methylation based classification was performed for both 450 k and 850 k data using the publically available “brain tumor classifier”, version v11b4 (https://www.molecularneuropathology.org/mnp) [7 (link)].