Infinium methylation 850k epic beadchip arrays

In the Chinese cohort, human DNA was extracted and purified from formalin-fixed paraffin-embedded (FFPE) tissues punches using QIAamp DNA FFPE Tissue Kit (QIAGEN, Cat No. Germany) according to the manufacturer’s instructions. The methylation of DNA was assayed on the Methylation 850K/EPIC Beadchip arrays (Illumina, San Diego, CA) using the Illumina HD methylation assay kit. It was performed at Shanghai Biotechnology Corporation following the manufacturer’s instructions. Total DNA (500 ng) was treated with bisulfate using an EZ DNA Methylation Gold Kit (Zymo Research, Irvine, CA).
In the German cohort, DNA was extracted from FFPE tissue using the Maxwell 16 FFPE Plus LEV DNA Kit (Promega, Madison, WI, USA), according to the manufacturer’s instructions. DNA concentration was quantified using the Qubit dsDNA BR Assay kit (Invitrogen, Carlsbad, CA, USA). Samples were analyzed at the Department of Neuropathology, Universitätsklinikum Heidelberg, Germany, using Illumina Infinium Methylation 850K/EPIC BeadChip arrays, as described previously [19 (link)]. Copy number profile analysis was assessed using the R package ‘conumee’ after an additional baseline correction (https://github.com/FAU-DLM/conumee).

Genomic DNA (500 ng) was bisulfite-converted using the EZ- DNA Methylation™ Kit (Zymo) according to manufacturer’s converted DNA was hybridized to the Illumina Infinium Methylation 850K EPIC BeadChip arrays (hereafter referred to as EPIC arrays). To avoid batch effects, samples were randomized on the EPIC arrays using the OSAT R package (16 (link)). Arrays were read using the iScan (Illumina™) to produce raw Idat files.{Campagna, 2022 #259}