Array-based DNA methylation profiling was accomplished by using the Illumina GoldenGate Cancer Panel I methylation bead array to simultaneously interrogate 1505 CpG loci associated with 807 cancer-related genes. We previously determined that this array showed high reproducibility; results obtained in FFPE tissues were highly correlated with those from matched non-FFPE samples (r =0.97), and published tumor-specific methylation profiles were detectable when DNA specimens contained at least 70% tumor cells [21 (link)].
Bead arrays were run in the Mammalian Genotyping Core laboratory at UNC at Chapel Hill. The Illumina GoldenGate methylation assay was performed as described previously [22 (link)] and imaged by using the BeadArray Scanner. Methylation status of the interrogated CpG sites was determined by comparing the ratio of the fluorescent signal from the methylated allele with the sum from the fluorescent signals of both methylated and unmethylated alleles. Controls for methylation status used on each bead array included the Zymo Universal Methylated DNA Standard as the positive, fully-methylated control, and a GenomePlex (Sigma-Aldrich, St. Louis, MO, USA) whole genome amplified DNA used as the negative, unmethylated control. Array data have been deposited in Gene Expression Omnibus under accession number GSE51557.
Bead arrays were run in the Mammalian Genotyping Core laboratory at UNC at Chapel Hill. The Illumina GoldenGate methylation assay was performed as described previously [22 (link)] and imaged by using the BeadArray Scanner. Methylation status of the interrogated CpG sites was determined by comparing the ratio of the fluorescent signal from the methylated allele with the sum from the fluorescent signals of both methylated and unmethylated alleles. Controls for methylation status used on each bead array included the Zymo Universal Methylated DNA Standard as the positive, fully-methylated control, and a GenomePlex (Sigma-Aldrich, St. Louis, MO, USA) whole genome amplified DNA used as the negative, unmethylated control. Array data have been deposited in Gene Expression Omnibus under accession number GSE51557.