Ffpe dna restoration kit

We used Illumina’s Infinium Methylation EPIC BeadChip following the manufacturer’s protocol for genome-wide methylation profiling. DNA extraction was performed using the Qiagen QIAamp DNA FFPE Tissue Kit. Purified DNA was quantified using the PicoGreen DNA quantification assay, stored at −20°C, and shipped via overnight shipping with dry ice packaging to the University of Southern California Core Facility for the methylation assay. At the Core Facility, purified DNA was bisulphite-converted (Zymo’s EZ DNA methylation kit), treated with a FFPE DNA Restoration Kit, and evaluated using Illumina’s FFPE QC Kit. The methylation status of the interrogated CpG site was presented as the β value, which is a continuous variable ranging from 0 (unmethylated) to 1 (fully methylated). To avoid confounding due to batch, BeadChip, or well position effects, we ensured that each case and his matched controls were included in the same batch and BeadChip. Samples within the case and matched controls were randomly assigned to well positions. Background correction and dye-bias normalization were performed at the USC core lab using the ‘noob’ function in the minfi R package. The ‘noob’ function corrects for background fluorescence intensities and red-green dye-bias[76 (link)].. The MethylationEPIC array targeted a total of 5273 CpGs from the 139 candidate genes.