DNA Methylation

DNA Methylation Analysis Simplified

The EpiTYPER^® workflow minimizes manual design and assay optimization that can lead to longer experimental time and unwanted variability.  EpiTYPER is an ideal solution for post-array and deep sequencing validation or targeted gene promoter analysis, providing you with:

Accurate and Reproducible DNA Methylation Mapping

• Individual methylation ratios for CpGs within a target sequence
• Relative methylation ratios between 10-90% with a standard deviation of 5%

Flexible DNA Methylation Experimental Design

• Scalable for investigating a few or several hundred regions over multiple samples
• Long reads up to 600 bp in one reaction enable discovery of differential methylation within large promoter regions
• Robust analysis from a range of sample types including Formalin Fixed Paraffin Embedded (FFPE) samples

EpiTYPER Overview

EpiTYPER Workflow

The EpiTYPER assay utilizes bisulfite converted DNA followed by PCR. Next, in vitro RNA transcription is performed on the reverse strand, followed by a base specific cleavage. The cleavage product results in a distinct signal pattern from the methylated and non-methylated template DNA that is automatically and quantitatively measured with the MassARRAY system. The resulting cleavage pattern depends on the presence of methylated cytosine in the original genomic DNA.  (See EpiTYPER Workflow.)

EpiBrowser

The EpiBrowser, a user-friendly tool, enables you to quickly display genes and samples of interest. EpiBrowser database allows you to view:

• Methylation status of CpG sites throughout the cancer related panel

• Validated primer sequences for amplifying regions of interest

Convenient Pre-Validated EpiPanels

• Standard EpiPanel: This panel includes 41 frequently studied genes. The panel offers the speed and convenience of using “off the shelf” validated assays to simplify and standardize methylation analysis. Download Standard EpiPanel

• Cancer EpiPanel: This panel targets 400 genes and over 12,000 CpG sites in promoter regions of genes known to be involved in neoplastic transformation and imprinting. The Cancer EpiPanel was used to produce quantitative DNA methylation profiles for more than 400 cancer related genes over 59 cell lines (NCI60) and normal tissues derived from 9 different tissue types (Ehrich et al. PNAS 2008). Browse Cancer EpiPanel

• Imprinting EpiPanel: This panel includes 31 pre-validated assays for the most commonly studied genes from which the methylation pattern is either paternally or maternally derived (Jirtle and Weidman, 2007).Download Imprinting EpiPanel

• Mouse Standard EpiPanel: This panel includes pre-validated assays for 182 genes. The panel offers the speed and convenience of using “off the shelf” validated assays to simplify and standardize methylation analysis. Download Mouse Standard EpiPanel

Custom DNA Methylation Assays with EpiDesigner Software 

If your gene(s) of interest are not included in the EpiPanels, you can easily design assays for any genomic region using the EpiDesigner Software. EpiDesigner is a free primer design tool that facilitates optimal primer design for amplifying bisulfite converted genomic regions of interest. Visit www.epidesigner.com to streamline your methylation studies.