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| Epigenetics
Epigenetic Modifi cation Analysis
Sequenom, Inc.
3595 John Hopkins Ct.
San Diego, CA 92121
aloria@sequenom.com
www.sequenom.com
858-202-9194
EpiTYPER for Quantitative DNA Methylation Analysis
EpiTYPER is a tool for the discovery and quantitative analysis of DNA
methylation that uses base specifi c cleavage and matrix-assisted
later desorption/ionization time-of-fl ight 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 bisulfi te treatment of genomic DNA, followed
by PCR amplifi cation in which a T7 promoter tag is introduced.
Next, in vitro RNA transcription is performed on the reverse strand,
followed by base specifi c 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.
References:
1. Clark, S., et al. Genomic Profiling of CpG Methylation and Allelic
Specificity Using Quantitative High-throughput Mass Spectrometry: Critical
Evaluation and Improvements. Nucleic Acid Research 2007; 1-14.
2. Held, W., et al. Identification of DNA Methylation in 3´ Genomic Regions
that Are Associated with Upregulation of Gene Expression in Colorectal
Cancer. Epigenetics 2007; 2(3).
3. Plass, C., et al. Downregulation of Death-Associated Protein Kinase 1
(DAPK1) in Chronic Lymphocytic Leukemia. Cell 2007; 129, 879-890.
Protocol Guide ı 2008 View entire protocol online at www.biotechniques.com/protocol ı BioTechniques ı 25
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