Patent ID: 7807358
Filing Date: 2010-10-05
Classification: C12Q

Abstract:
1. A process of identifying methylation patterns in DNA from a cell sample, said process comprising: a) isolating a first set of amplicons comprising (i) contacting genomic DNA derived from a tumor cell with an enzyme that is not methylation-sensitive, lacks a CpG dinucleotide sequence in its recognition motif, and that cleaves the genomic DNA into fragments in which CpG islands are preserved and which have ends corresponding to the cleavage motif of the non-methylation-sensitive enzyme; (ii) ligating the fragments, via the ends corresponding to the cleavage motif of the non-methylation sensitive enzyme, to linker primers to form linker primer fragments; (iii) contacting the linker primer fragments with a methylation-sensitive enzyme which digests the linker primer fragments 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; (iv) amplifying the digestion product to form amplicons of the methylated CpG island loci; and (v) labeling the amplicons; b) isolating a second set of amplicons comprising repeating (i) through (v) of step (a) wherein the genomic DNA of (i) is genomic DNA derived from a non-tumor cell; c) contacting the first set of amplicons with a first screening array comprising a plurality of nucleic acid fragments affixed to a solid support and determining the presence or absence of labeled amplicons bound to the plurality of nucleic acid fragments of the first screening array; d) contacting the second set of amplicons with a second screening array comprising a plurality of nucleic acid fragments affixed to a solid support wherein said plurality of nucleic acid fragments of the second screening array is identical to the plurality of nucleic acid fragments of the first screening array and determining the presence or absence of labeled amplicons bound to the plurality of nucleic acid fragments of the second screening array; and e) observing whether the presence or absence of the first set of amplicons bound to the plurality of nucleic acid fragments of the first screening array is the same as the presence or absence of the second set of amplicons bound to the plurality of the nucleic acid fragments of the second screening array, thereby identifying methylation patterns in DNA from a cell sample.