Loci-Specific DNA Methylation

Gene Specific DNA Methylation

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.

EpigenDx Gene Specific DNA Methylation

Step One | Selecting a Pyrosequencing Target

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

Promoter Region of Human GCR (NR3C1) chart

Description: 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.

Step Two | 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.

Item No. Service Service Description Price

DNA Methylation Analysis

Quantitative Methylation Analysis on submitted bisulfite-converted PCR products

  • Perform Pyrosequencing run & methylation analysis ONLY
8002 Standard Plus

DNA Methylation Analysis

Quantitative Methylation Analysis

  • Bisulfite PCR using analytically validated assay
  • Pyrosequencing sample preparation: making ssDNA template for Pyrosequencing
  • Setup Pyrosequencing, and run Pyrosequencing
  • Pyrosequencing run QC: Pass E & S, negative dispensation, incomplete bisulfite modification, and correct sequence pattern

Step Three | 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.

Interpretation of Data

Methylation data can then be applied to research. For example, normal healthy individuals maintain high methylation levels (75-85%) in the LINE-1 elements to suppress retrotransposons that would otherwise copy and transpose themselves erratically across the genome. Abnormally low methylation in the LINE elements have been shown to be common in many malignancies, due to genomic instability.

EpigenDx - methylation of ovarian tissue_cmyc2_chart
Speak with experts at EpigenDx for high quality technical support and consultation through all phases of the project, from assay design to data delivery.

Working With Us Is Easy

EpigenDx idea icon

Tell Us About Your Project

EpigenDx mail icon

Send Us Your Sample

EpigenDx laboratory icon

Receive Your Data

Can’t Locate Your Region Of Interest?

No problem, we’ve got you covered. EpigenDx provides custom assay design and analytical services with an assay database of thousands of Off-the-Shelf designs ready to go. Not only do we provide aggressive timelines with regular project updates, you will also get the highest quality technical support and consultation from design phase through project completion and data delivery.


Experts in DNA Methylation

Now Offering GLP and GCP Compliant Laboratory Services

EpigenDx Offers Many Customized Services