Process for high throughput DNA methylation analysis
First Claim
1. A method for detecting cytosine methylation and methylated CpG islands within a genomic sample of DNA comprising:
- (a) contacting a genomic sample of DNA with a modifying agent that modifies unmethylated cytosine to produce a converted nucleic acid;
(b) amplifying the converted nucleic acid by means of oligonucleotide primers in the presence of one or a plurality of specific oligonucleotide probes, wherein one or a plurality of the oligonucleotide primers or the specific probe(s) are capable of distinguishing between unmethylated and methylated nucleic acid, with the proviso that at least one oligonucleotide probe is a CpG-specific probe capable of distinguishing between unmethylated and methylated nucleic acid; and
(c) detecting, in real-time during the amplification, the methylated nucleic acid based on amplification-mediated probe displacement.
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Abstract
There is disclosed an improved high-throughput and quantitative process for determining methylation patterns in genomic DNA samples based on amplifying modified nucleic acid, and detecting methylated nucleic acid based on amplification-dependent displacement of specifically annealed hybridization probes. Specifically, the inventive process provides for treating genomic DNA samples with sodium bisulfite to create methylation-dependent sequence differences, followed by detection with fluorescence-based quantitative PCR techniques. The process is particularly well suited for the rapid analysis of a large number of nucleic acid samples, such as those from collections of tumor tissues.
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Citations
43 Claims
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1. A method for detecting cytosine methylation and methylated CpG islands within a genomic sample of DNA comprising:
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(a) contacting a genomic sample of DNA with a modifying agent that modifies unmethylated cytosine to produce a converted nucleic acid; (b) amplifying the converted nucleic acid by means of oligonucleotide primers in the presence of one or a plurality of specific oligonucleotide probes, wherein one or a plurality of the oligonucleotide primers or the specific probe(s) are capable of distinguishing between unmethylated and methylated nucleic acid, with the proviso that at least one oligonucleotide probe is a CpG-specific probe capable of distinguishing between unmethylated and methylated nucleic acid; and (c) detecting, in real-time during the amplification, the methylated nucleic acid based on amplification-mediated probe displacement. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11)
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12. A method for detecting a methylated CpG-containing nucleic acid comprising:
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(a) contacting a nucleic acid-containing sample with a modifying agent that modifies unmethylated cytosine to produce a converted nucleic acid; (b) amplifying the converted nucleic acid in the sample by means of oligonucleotide primers in the presence of a CpG-specific oligonucleotide probe, wherein the CpG-specific probe, but not the primers, distinguishes between modified unmethylated and methylated nucleic acid; and (c) detecting, in real-time during the amplification, the methylated nucleic acid based on amplification-mediated probe displacement. - View Dependent Claims (13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23)
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24. A method for detecting a methylated CpG-containing nucleic acid comprising:
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(a) contacting a nucleic acid-containing sample with a modifying agent that modifies unmethylated cytosine to produce a converted nucleic acid; (b) amplifying the converted nucleic acid in the sample by means of oligonucleotide primers in the presence of a CpG-specific oligonucleotide probe, wherein both the primers and the CpG-specific probe distinguish between modified unmethylated and methylated nucleic acid; and (c) detecting, in real-time during the amplification, the methylated nucleic acid based on amplification-mediated probe displacement. - View Dependent Claims (25, 26, 27, 28, 29, 30, 31, 32, 33, 34)
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35. A method for detecting cytosine methylation within a genomic sample of DNA, comprising:
- obtaining a methylation kit;
conducting, using the kit, a real-time methylation assay of the genomic DNA sample; and
determining, based on the methylation assay, whether cytosine methylation is present in the DNA sample, and wherein the methylation kit comprises;a modifying agent that modifies unmethylated cytosine to produce a converted nucleic acid; primers for amplification of the converted nucleic acid; primers for the amplification of control unmodified nucleic acid; and a CpG-specific probe the detection of which, during the amplification of the converted nucleic acid, is in real-time based on amplification-mediated probe displacement, wherein the CpG-specific probe distinguishes between modified unmethylated and methylated nucleic acid, and wherein the primers each may or may not distinguish between unmethylated and methylated nucleic acid. - View Dependent Claims (36, 37, 38, 39, 40, 41, 42, 43)
- obtaining a methylation kit;
Specification