Gene Specific DNA Methylation

Service Description

Analysis of the percentage methylation levels of all consecutive CpG sites within a gene locus.

Since DNA methylation is frequently heterogeneous within a sample, it is important to quantify the relative proportion of methylated and unmethylated alleles at each CpG site. We achieve this by direct Pyrosequencing after bisulfite modification and PCR amplification.

All of our assays are pre-validated to ensure there is no preferential amplification for either methylated or unmethylated DNA, allowing us to provide the highest quality data and results. EpigenDx has almost 15 years of expertise in epigenetics using Pyrosequencing technology.

CpG Methylation

Step 1: Selecting a Pyrosequencing Target

Search For Your Gene of Interest:
  • A rapidly growing database of over 7000 validated assays (ADS) for human, mouse, and rat gene loci.
  • Contact us and ask to the see the Assay Information Report for detailed information.

Figure 1: Promoter Region of Human GCR (NR3C1) (Ensembl Transcript: ENST00000231509)

CpG Coverage of a Gene
Figure 1: This is an example of EpigenDx’s CpG site coverage in a typical gene such as Human GCR. Red markers are CpG sites covered by at least one of EpigenDx’s pre-developed assays (ADS). Blue X’s are all other CpG sites.

Off-The-Shelf Methylation Assays

Custom Assay Design
  • Can’t locate your region of interest?
  • EpigenDx does custom assay design. Send us your sequence and we’ll develop the assay.

Step 2: Choose an Ideal Plan for You

All parts of our methylation services are customizable and modular. Pick and choose the service plan that is appropriate and ideal for your needs.

Items Service Products Description Order
8001 DNA Methylation Analysis – Standard Quantitative Methylation Analysis on submitted bisulfite-converted PCR products

  • Perform Pyrosequencing run & methylation analysis ONLY
 Inquiry / Order
8002 DNA Methylation Analysis – Gold Quantitative Methylation Analysis on submitted bisulfite modified DNA

  • Perform PCR reactions
  • Perform Pyrosequencing methylation analysis
 Inquiry / Order
8003 DNA Methylation Analysis – Premium Quantitative Methylation Analysis on submitted genomic DNA

  • Perform bisulfite modification
  • Perform PCR reactions
  • Perform Pyrosequencing analysis
 Inquiry / Order

Turn-around time is 5-15 days for most DNA methylation services, depending the number of assays and samples sent. Click here for a detailed breakdown of EpigenDx’s methylation service workflow.

Step 3: Results

EpigenDx analyzes the raw data and delivers:

  • The percentage methylation values of each CpG site in a Microsoft Excel spreadsheet.
  • The raw pyrograms in a PDF document.
    • Sample Application of DNA Methylation Data

    Interpretation of Data

    Methylation data can then be applied to research. For example, increased DNA methylation at specific CpG sites in the promoter region of genes is a hallmark of many cancers.

    Speak with experts at EpigenDx for high quality technical support and consultation through all phases of the project, from assay design to data delivery.