Method of characterizing ZDHHC1 DNA
View Patent ↗Provided herein is technology relating compositions and methods for detecting tissue cell-specific DNA, such as epithelial cell-specific DNA, in blood or blood products from a subject. The technology also relates to use of tissue cell-specific DNAs as internal controls for methylation assays.
1. A method of characterizing blood or blood product, comprising:
a) providing a blood or blood product sample from a subject;
b) assaying said sample to detect the presence of ZDHHC1 epithelial cell-specific DNA,
wherein said assaying comprises:
i) treating DNA from said sample with a bisulfite reagent to create bisulfite-converted ZDHHC1 DNA comprising the nucleotide sequence of SEQ ID NO:33;
ii) amplifying a region of said bisulfite converted DNA using a pair of primers complementary to primer binding sites within SEQ ID NO:27 and its complement, wherein in said amplifying, said primers hybridize to said primer binding sites and are extended to amplify a region of SEQ ID NO:27 bounded by the primer binding sites to produce amplified product; and
iii) detecting said amplified product.
2. The method of claim 1 , wherein said blood product is plasma.
3. The method of claim 1 , wherein said detecting comprises detecting hybridization of the amplified product to a detection probe.
4. The method of claim 3 , wherein said detection probe comprises a reporter molecule.
5. The method of claim 4 , where said reporter molecule comprises a fluorophore.
6. The method of claim 3 , wherein said detection probe comprises a flap sequence.
7. The method of claim 3 , wherein said detecting hybridization of the amplified product to said detection probe comprises use of a FRET cassette.
8. The method of claim 3 , wherein said detecting hybridization of the amplified product to said detection probe comprises use of a FEN-1 endonuclease.
9. The method of claim 1 , wherein assaying said sample comprises measuring an amount of ZDHHC1 epithelial cell-specific DNA in the blood or blood product sample.
10. The method of claim 9 , wherein said measuring comprises a quantitative amplification reaction.
11. The method of claim 10 , wherein the quantitative amplification reaction comprises real-time fluorescence detection.