Patent ID: 8361724

Claim:
A method for analyzing the methylation status of a target sequence in a sample with an internal control for detecting the presence of the target sequence, the method comprising: (a) providing a sample that includes DNA; (b) optionally, purifying the DNA from the sample to thereby produce purified DNA; (c) optionally, amplifying the DNA and simultaneously copying the methylation pattern of the DNA to thereby produce amplified DNA; (d) treating the sample, purified DNA, or amplified DNA with a methylase that preferentially methylates at one or more control sequence nucleotides in a target sequence that is present in the DNA before the DNA is optionally amplified, wherein the one or more control sequence nucleotides are cytosines present in the target sequence before the DNA is optionally amplified and wherein (i) the methylase preferentially methylates cytosines other than cytosines in CpG dinucleotides or (ii) the methylase has a recognition sequence which is larger than a CpG dinucleotide; and (e) assaying the sample, purified DNA, or amplified DNA for the methylation status of (i) the one or more control sequence nucleotides and (ii) one or more CpG dinucleotides in the target sequence; wherein the target sequence is in the sample and wherein (a′) methylation at the one or more control sequence nucleotides indicates the presence of the target sequence in the sample before the DNA from the sample is optionally amplified, and the presence or absence of methylation at the one or more CpG dinucleotides indicates the presence or absence, respectively, of methylation at the corresponding dinucleotides in the sample, or (b′) absence of methylation at the one or more control sequence nucleotides indicates the absence of the target sequence in the sample, purified DNA, or amplified DNA and/or a technical failure.