Methods for detecting methylated nucleotides
First Claim
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1. A method for detecting methylated nucleotides within a nucleic acid sample, comprising:
- splitting a nucleic acid sample into separate reaction vessels;
contacting nucleic acid molecules in one reaction vessel with bisulfite;
amplifying the nucleic acid molecules in each reaction vessel in the presence of dUTP;
cleaving the amplified nucleic acid molecules in each reaction vessel at uracil to produce fragments thereof; and
obtaining a mass spectrum of the resulting fragments from one reaction vessel and another mass spectrum of the resulting fragments from another reaction vessel, whereby;
cytosine methylation is detected by identifying a difference in signals between the mass spectra thereby detecting methylated nucleotides.
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Abstract
A method for detecting methylated nucleotides within a nucleic acid sample is provided. The method includes the steps of splitting a nucleic acid sample into separate reaction vessels; contacting nucleic acid in one reaction vessel with bisulfite; amplifying the nucleic acid in each reaction vessel; cleaving the nucleic acids in each reaction vessel to produce fragments thereof; and obtaining a mass spectrum of the resulting fragments from one reaction vessel and another mass spectrum of the resulting fragments from another reaction vessel.
142 Citations
13 Claims
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1. A method for detecting methylated nucleotides within a nucleic acid sample, comprising:
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splitting a nucleic acid sample into separate reaction vessels; contacting nucleic acid molecules in one reaction vessel with bisulfite; amplifying the nucleic acid molecules in each reaction vessel in the presence of dUTP; cleaving the amplified nucleic acid molecules in each reaction vessel at uracil to produce fragments thereof; and obtaining a mass spectrum of the resulting fragments from one reaction vessel and another mass spectrum of the resulting fragments from another reaction vessel, whereby; cytosine methylation is detected by identifying a difference in signals between the mass spectra thereby detecting methylated nucleotides. - View Dependent Claims (2, 3, 4, 5)
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6. A method for detecting methylated nucleotides within a nucleic acid sample, comprising:
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treating nucleic acid molecules with bisulfite to deaminate any unmethylated cytosine to produce uracil; amplifying the treated nucleic acid molecules in the presence of dUTP; fragmenting the amplified treated nucleic acid molecules by cleavage at uracil; obtaining a mass spectrum of the fragmented amplified treated nucleic acid molecules; obtaining a mass spectrum of fragmented amplified untreated nucleic acid molecules; and identifying the fragments of amplified treated nucleic acid molecules that contain uracil in place of cytosine by comparing the spectrum from amplified treated fragments with a spectrum resulting from amplified untreated nucleic acid molecules thereby detecting methylated nucleotides. - View Dependent Claims (7, 8)
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9. A method for detecting methylated nucleotides within a nucleic acid sample, comprising:
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treating nucleic acid molecules with bisulfite to deaminate any unmethylated cytosine to produce uracil; amplifying the treated nucleic acid molecules in the presence of dUTP; fragmenting the amplified treated nucleic acid molecules by cleavage at uracil; obtaining a mass spectrum of the fragmented amplified treated nucleic acid molecules; obtaining a mass spectrum of fragmented amplified untreated nucleic acid molecules; and comparing the spectrum from amplified treated fragments with the spectrum from amplified untreated nucleic acid molecules; whereby the presence of at least one methylated cytosine is detected thereby detecting methylated nucleotides. - View Dependent Claims (10, 11)
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12. A method for identifying the absence, presence or frequency of a polymorphism in a population, wherein said polymorphism is manifested or detected as a difference in post-translational modification, which comprises:
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pooling genomic nucleic acid molecules isolated from body tissue or fluid from a plurality of individuals; treating the nucleic acid molecules with bisulfite to deaminate any unmethylated cytosine to produce uracil; amplifying the treated nucleic acid molecules; cleaving the amplified treated nucleic acid molecules at uracil, to produce fragments thereof; obtaining a mass spectrum of the fragmented amplified treated nucleic acid molecules; obtaining a mass spectrum of fragmented amplified untreated nucleic acid molecules; identifying the fragments of amplified treated nucleic acid molecules that contain uracil in place of cytosine by comparing the spectrum from treated amplified treated fragments with a spectrum resulting from amplified untreated nucleic acid molecules and identifying the absence, presence, or frequency of a polymorphism by determining the allelic frequency of allelic fragments obtained from the pooled genomic nucleic acid molecules. - View Dependent Claims (13)
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Specification