ObjectivePrader-Willi syndrome (PWS) is a complex, multisystem disorder, which is difficult to be diagnosed based on clinical symptoms and the purpose of this study is to establish methylation-specific PCR (MS-PCR) assay for the diagnosis of PWS, and evaluate its use in clinical cases. MS-PCR assay has been developed abroad for 10 years, and it is efficient, fast, specific and sensitive but it has not yet been used in clinical diagnosis in our country.MethodsForty-four subjects were assigned to 3 groups: normal controls (n=16), typical PWS patients (n=7) and suspected PWS patients (n=21). Genome DNA was extracted by salt fractionation method and treated with CpGemoneTM Fast Modification Kit. Using unmodified genome DNA as system control, the modified DNA was amplified by PCR with two primer pairs (M and P), and separated by agarose gel electrophoresis.ResultsAll normal controls showed both 174 bp (M) and 100 bp (P) products, while all of the seven typical PWS patients demonstrated only 174 bp (M) product. In the 21 suspected patients, two cases were confirmed with PWS by MS-PCR, while others were excluded from PWS. ConclusionsMS-PCR appears to be a specific, efficient and convenient assay for the diagnosis of PWS.