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Epigenetic Analysis/DNA Methylation

Sequenom Epigenetic Analysis

Description
Sequenom epigenetic analysis (called EpiTYPER) is designed for high-throughput quantitative DNA methylation analysis and for discrimination between methylated and non-methylated samples. It is ideal for the investigation of a few to several hundred regions over multiple samples, and it allows you to accurately and precisely analyze multiple CpGs in amplicons of up to 600bp. This technology is also highly sensitive, with the ability to detect a 5% change in methylation levels from as little as 5pg of starting material. The accompanying software provides convenient data analysis and export. (Source: Sequenom.com)

Science
Sequenom epigenetic analysis combines base-specific enzymatic cleavage and MALDI-TOF mass spectrometry for high-throughput quantitative DNA methylation analysis. The protocol begins with a bisulfite treatment of genomic DNA, which converts non-methylated cytosine into uracil. This treatment is followed by PCR amplification with T7-promotor tagged primers, which bind to both methylated and non-methylated template and provide an appropriate product for in vitro transcription. Next, in vitro RNA transcription is performed on the reverse strand to generate a transcript that is then subjected to base-specific cleavage. The C/T variations from the bisulfite treatment appear as G/A variations in the cleavage products, resulting in a mass difference of 16 Da per CpG site. MALDI-TOF MS analyzes the fragments, and the EpiTYPER software generates quantitative results for each analyzed product. (Source: Ehrich, M., Correll, D., Van den Boom, Dirk, 2006, Introduction to EpiTYPER for Quantitative DNA Methylation Analysis Using the MassARRAY System, SEQUENOM, Doc. No. 8876-007).

Protocol
(Protocol not yet available.)

Pricing
Contact Core personnel to receive a quote for this service.

What to Provide
Please contact Core personnel.

Additional Resources
A searchable database of core facilities at all UCSF campus locations, provided by the Clinical and Translational Science Institute at UCSF, is available here.