Hd methylation assay kit

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).

Converted DNA was used for hybridization on an Illumina Infinium 850K Methylation BeadChip array (Illumina, San Diego, CA), and an Illumina HD methylation assay kit (Shanghai Biotechnology Corporation) was used to assay DNA methylation levels. After quality filtering and data normalization, differentially methylated CpGs between HCC and normal liver tissues were screened using the R package IMA. We used the mean difference in β-value (Δβ) between the two abovementioned groups to evaluate the methylation level for each CpG site. CpG sites that showed |∆β|> 0.1 and p value < 0.05 were defined as significantly differentially methylated sites.