DNA Methylation Profiling Using Illumina Beadchips

DNA was isolated from peripheral blood leukocytes obtained from stored blood samples, and was bisulfite-converted with the EZ DNA Methylation Gold Kit (Zymo Research, Orange CA). Bisulfite-converted DNA samples were whole-genome amplified, enzymatically fragmented, and purified, then hybridized to Illumina Infinium HumanMethylation27BeadChips, which contain locus-specific DNA oligomers and a set of 56 control probes. The array was then fluorescently stained, scanned using the Illumina BeadXpress reader, and assessed for fluorescence intensities across the methylated and unmethylated bead types at 27,578 CpG sites [31 (link)–33 (link)]. This work was performed at the Genotyping Core in the Mayo Clinic Advanced Genomics Technology Center (Rochester, MN).