Objective  To compare the diagnostic effectiveness of methylation-specific PCR (MS-PCR) and methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) in clinical suspected Prader-Willi syndrome (PWS).

  Methods  One hundred and two participants (57 males and 45 females) who visited Peking Union Medical College Hospital in the period from October 2005 to February 2014 were included inthis retrospective study. Among the 102 participants, 16 were normal controls, 2 PWS cases confirmed by fluorescence in situ hybridization or high resolutin banding were positive controls, and 84 were suspected PWS cases. Genomic DNA was extracted for MS-PCR and MS-MLPA, based on which diagnoses were made and genetic types distinguished. Chi-squared test was used to compare the sensitivity, specificity, and accuracy of the two methods.

  Results  MS-PCR results showed that all normal controls and positive controls were conform to their phenotypes. Thirty-nine in the 84 suspected patients were shown to be PWS, and the other 45 to be normal. MS-MLPA showed that in the 86 non-normal participants (positive control and suspected cases), 29 had paternal deletions, 9 had maternal uniparental disomy (mUPD), 47 were normal; and the assay failed to produce effective result in 1 case due to the overlong DNA storage time. Two participants were diagnosed as PWS cases by MS-PCR but normal by MS-MLPA. The diagnosis of PWS was ruled out by repeat MS-PCR after doubling DNA dosage. Combined with clinical manifestations, 39 participants were definitively diagnosed as PWS, the other 63 were not PWS. The false-positive rate of MS-PCR was 3.17%(2/63).The sensitivity, specificity, and accuracy of MS-PCR were 100%, 96.83%, and 98.03%, respectively; while those indicators of MS-MLPA were 97.43%, 100%, and 99.02%, respectively, showing no significant difference (all P > 0.05).

  Conclusions  Both MS-PCR and MS-MLPA have high sensitivity, specificity, and accuracy, thus are effective for PWS diagnosis. MS-MLPA can distinguish paternal deletion and mUPD. Enough dose of DNA is requisite in MS-PCR to avoid false-positive results. Freshness of DNA samples is essential in MS-MLPA, which also needs more strict performance standards. We suggest a combination of MS-PCR and MS-MLPA in diagnosing PWS to ensure the accuracy of the result.