High-throughput methods for detecting DNA methylation

A process for detecting the presence or absence of methylation of CpG dinucleotide rich regions of nucleic acid sequences within a genomic DNA sample, the process comprising:

• a) contacting the genomic DNA sample with an enzyme that is not methylation-sensitive, but which cleaves the nucleic acid sequences into fragments in which CpG islands are preserved and which have ends corresponding to the cleavage motif of the non methylation sensitive enzyme;
• b) ligating the fragments, via the ends corresponding to the cleavage motif of the non methylation sensitive enzyme, to linker primers to form ligated linker primer products;
• c) contacting the ligated linker primer products with a methylation-sensitive enzyme which digests the ligated linker primer products having unmethylated CpG dinucleotide sequences but not methylated CpG dinucleotide sequences to form a digestion product comprising methylated CpG island loci, and wherein fragments cleaved by the methylation-sensitive enzyme are rendered non-amplifiable by the linker primers;
• d) amplifying the digestion product to form amplicons of the methylated CpG island loci;
• e) labeling the amplicons;
• f) contacting the labeled amplicons with a screening array comprising a plurality of nucleic acid fragments affixed to a solid support;
• and
• g) determining the presence or absence of labeled amplicons bound to the plurality of nucleic acid fragments affixed to the solid support of the screening array to thereby detect the presence or absence of methylation of CpG dinucleotide rich regions.