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EpiTYPER for Quantitative DNA Methylation Analysis
Sponsored,vendor-submitted protocol   Sponsored by Sequenom    Published in BioTechniques Protocol Guide 2008 (p.25)

EpiTYPER is a tool for the discovery and quantitative analysis of DNA methylation that uses base specific cleavage and matrix-assisted later desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Using the speed and accuracy of the MassARRAY® system, this method is ideal for discovery of methylation, for discrimination between methylated and non-methylated samples, and for quantifying the methylation levels of DNA.

The method starts with bisulfite treatment of genomic DNA, followed by PCR amplification in which a T7 promoter tag is introduced. Next, in vitro RNA transcription is performed on the reverse strand, followed by base specific cleavage. MALDI-TOF MS analysis of the cleavage products results in a distinct signal pair pattern from the methylated and non-methylated template DNA.

Information presented in the mass spectrum can be used to assess the degree of methylation for each CpG unit independently or to estimate the average methylation for the entire target region. Using this method, both hypermethylation and hypomethylation can be detected in samples. The MassARRAY system is able to detect the methylation level in a mixture as low as 5%.

This pane provides a graphical representation of the CpG sites within the selected amplicon. Each is color-coded to the degree of methylation to allow quick, reliable comparison between samples and CpG sites.

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