Microarray analysis of DNA methylation targets identified by methyl-CpG-binding proteins

We propose the combined use of methyl-CpG-binding domain (MBD) column chromatography and microarray technologies for interrogating cancer genomes. The MBD column chromatograph is based on the affinity binding of methylated CpG island targets to individual MBD proteins and is used to selectively elute bound DNA fragments. The approach is shown to be effective for identifying a large number of methylated loci in the cancer genome. To increase throughput, cloned DNA fragments can further be spotted on microarray slides for differential methylation hybridization. Fluorescently labeled amplicons, which represent different pools of methylated DNA fragments in tumor and control samples, are prepared and cohybridized onto a microarray slide. Methylated loci are identified based on their differential fluorescence intensities in tumors relative to the control samples. Hierarchical clustering algorithms are further employed to segregate tumor subgroups showing similar methylation profiles. Such a microarray-based analysis, which uses cloned methylated loci by the MBD technology, can routinely be used for clinical diagnosis of specific cancer types.