Targeted NGS Methylation Analysis

Targeted Next-Gen Bisulfite Sequencing for DNA Methylation Analysis

NGS Next-Gen Sequencing

EpigenDx specializes in targeted next-generation sequencing (NGS) services for affordable, fast, and precise sequencing of custom target regions. Our targeted bisulfite sequencing services can provide methylation data for dozens of genes and entire promoter regions in a single run.

Choose from pre-validated panels or utilize our design services to develop a custom library covering your targets of interest. All of our off-the-shelf panels are validated with Pyrosequencing technology.

We use Ion Torrent™ technology for targeted gene sequencing and methylation analysis.


Targeted Next-Gen Bisulfite Sequencing is more economical and has a faster turnaround time than whole-genome methylation analysis (WGBS or RRBS). It allows you to analyze only the regions and genes you are interested in, and produces higher quality data due to significantly greater coverage of each CpG site.

EpigenDx offers a complete solution for targeted NGS. We perform the DNA extraction, bisulfite modification, library preparation, high throughput sequencing, data analysis, and assay validation with Pyrosequencing. We are the experts in DNA methylation analysis with over 15 years of experience in bisulfite sequencing.


DNA Methylation Analysis
  • Measure the percent methylation of multiple target regions (PCR amplicons) and multiple samples in a single run.
  • Ability to perform DNA methylation analysis covering many areas of one gene or a diverse set of regions across multiple genes
Illumina’s MethylationEPIC BeadChip Assay Validation

Pre-Designed Methylation Panels

Use our pre-validated off-the-shelf methylation panels to assess the methylation levels of genes related to cancer, pluripotency, and more.

Custom Panel Design

Send us custom target regions with your genes of interest. We will design and validate a custom panel of assays.

Our Services:

Items Service Products Description Order
8200 Custom NGS Assay Design Assay design based on customer-submitted target region(s).

  • Includes the cost of oligos.
Inquiry / Order
8500 Targeted Next-Gen Sequencing – Standard Custom target gene sequencing using Ion Torrent instruments:

  • Customer provides the PCR amplicons
  • EpigenDx constructs the library and performs Next-Gen Sequencing
Inquiry / Order
8501 Targeted Next-Gen Sequencing – Premium Custom target gene sequencing using Ion Torrent instruments:

  • Customer provides tissue samples or isolated DNA
  • EpigenDx performs:
    • DNA extraction
    • Bisulfite modification
    • Multiplex PCR
    • Library construction
    • Next-Gen Sequencing
Inquiry / Order
8100a NGS Data Analysis Preliminary data analysis of NGS generated sequencing data. Inquiry / Order