Patent ID: 8748100

Claim:
A method for selectively amplifying a hypomethylated target DNA fragment which has been cut by a methylation-sensitive restriction enzyme in a sample containing a corresponding hypermethylated DNA fragment which is not cut by the enzyme, the method comprising: (a) contacting the sample with a stem-loop primer, wherein the 3′ portion of the stem-loop primer is complementary to the 3′ end of a strand of the hypomethylated target DNA fragment at the cut site, and the 5′ portion of the stem-loop primer is capable of forming a stem-loop structure; (b) annealing the stem-loop primer to the strand of the hypomethylated DNA fragment via the 3′ portion thereof and performing an extension reaction by using the strand of the hypomethylated DNA fragment as a template; and (c) amplifying the extension product to obtain an amplified product of the hypomethylated target DNA fragment, wherein the hypomethylated target DNA fragment is at least a part of CGI137, phosphodiesterase 9A (PDE9A), Homo sapiens protein phosphatase 1, regulatory (inhibitor) subunit 2 pseudogene 2 (PPP1R2P2), or Similarity to Fem1A ( Caenorhabditis elegans ).