We have developed a new generation of genome-wide DNA methylation BeadChip which allows high-throughput methylation profiling of the human genome. The new high density BeadChip can assay over 480K CpG sites and analyze twelve samples in parallel. The innovative content includes coverage of 99% of RefSeq genes with multiple probes per gene, 96% of CpG islands from the UCSC database, CpG island shores and additional content selected from whole-genome bisulfite sequencing data and input from DNA methylation experts. The well-characterized Infinium® Assay is used for analysis of CpG methylation using bisulfite-converted genomic DNA. We applied this technology to analyze DNA methylation in normal and tumor DNA samples and compared results with whole-genome bisulfite sequencing (WGBS) data obtained for the same samples. Highly comparable DNA methylation profiles were generated by the array and sequencing methods (average R2 of 0.95). The ability to determine genome-wide methylation patterns will rapidly advance methylation research.

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Aberrations in DNA methylation patterns are widely recognized as a hallmark of the cancer cell. DNA methylation has emerged as a promising biomarker for the detection and classification of various types of cancer, and ability to accurately assess the DNA methylation changes plays an important role in understanding of disease onset and progression. We developed a new generation of genome-wide DNA methylation BeadChip which allows high-throughput methylation profiling of human genome. The new high density BeadChip can assay over 480K CpG sites and analyze twelve samples in parallel. The innovative content includes coverage of 99% of RefSeq genes with multiple probes per gene, 96% of CpG islands from the UCSC database, CpG island shores and additional content selected from whole-genome bisulfite sequencing data and input from DNA methylation experts. The well-characterized Infinium® assay is used for analysis of CpG methylation using bisulfite-converted genomic DNA. In this assay, unmethylated cytosines (C) are converted to uracil (U) when treated with bisulfite, while methylated cytosines remain unchanged. The assay design is using single probe assays for CpG loci with up to two underlying CpG dinucleotides, and two-probe assays for CpG loci with multiple underlying CpG sites, with one probe querying the “unmethylated” allele and the other probe querying the “methylated” allele. The assays are designed under the assumption that methylation is regionally correlated (within 50 base pairs) and that all CpG sites underlying the probe are assumed to be “in phase” with the queried CpG site. For the BeadChip development, we used methylation standards created by de-methylating gDNA with Phi29 whole genome amplification, methylating the amplified DNA with SssI methylase and mixing the unmethylated and methylated DNA in a 1:1 ratio to create a 50% methylation state. 500 ng gDNA input is used for bisulfite conversion and is sufficient for two assays. Reproducible DNA methylation profiles were obtained between replicates (an average R2 of 0.98). We applied this technology to DNA methylation analyses in cancer cell lines of different tissue of origin and normal DNA samples derived from multiple tissues. Highly specific methylation signatures were obtained for each sample type. The ability to determine genome-wide methylation patterns will rapidly advance methylation research and ultimately lead to the development of powerful tools for diagnosis, prognosis, and treatment of human diseases. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr LB-176. doi:10.1158/1538-7445.AM2011-LB-176