Methods and compositions for detecting cancers associated with methylation of hmlh1 promoter dna

Abstract

Methods are provided for detection of cancers associated with methylation of hMLH1 promoter DNA in a subject. The method comprise assaying for the presence of methylated hMLH1 promoter DNA in a bodily fluid from a subject. In one embodiment, the method comprises reacting DNA from the sample with a chemical compound that converts non-methylated cytosine bases but not methylated cytosine bases, to a different nucleotide base. The compound-converted DNA is then amplified using a methylation-sensitive polymerase chain reaction (MSP) employing primers that amplify the compound-converted DNA template. The present invention also provides nucleotide primer sequences for use in the methylation-sensitive PCR assay.

1 - 35 . (canceled) 
     
     
         36 . A primer for detecting methylation of human mutL homolog 1 (hMLH1) promoter DNA, wherein said primer is at least 15 nucleotides in length and anneals to a bisulfite-converted template sequence located between base pairs 1264 and 1354 in SEQ ID NO: 1, or a complement thereof, wherein said primer is selected from the group consisting of: a primer comprising at least 8 consecutive nucleotides in SEQ ID NO: 2, and a primer comprising at least 8 consecutive nucleotides in SEQ ID NO: 3. 
     
     
         37 . The primer of  claim 36 , wherein the primer comprises a CpG dinucleotide. 
     
     
         38 . The primer of  claim 36 , wherein the primer is selected from a forward primer and a reverse primer. 
     
     
         39 . The primer of  claim 36 , wherein said primer is labeled with a fluorescent dye. 
     
     
         40 . The primer of  claim 36 , wherein the primer is selected from a forward primer comprising at least 8 consecutive nucleotides in SEQ ID NO: 5 and a reverse primer comprising at least 8 consecutive nucleotides in SEQ ID NO: 6. 
     
     
         41 . The primer of  claim 36 , wherein said primer has the sequence of SEQ ID NO: 2. 
     
     
         42 . The primer of  claim 36 , wherein said primer has the sequence of SEQ ID NO: 3.