Methylation Controls

Scientific Overview

Keep your DNA methylation experiments in control. EpigenDx offers methylated genomic DNA controls to serve as positive or negative controls in DNA methylation analysis experiments. The controls have been used on more than 14,000 gene-specific and global methylation assays using targeted bisulfite NGS (tNGBS), Pyrosequencing, and MS-HRM. They are recommended for use in DNA methylation assay development, optimization, and validation to ensure assay linearity, specificity, and reproducibility for research and clinical applications.

Available in human, mouse, rat, monkey, as well as custom species.

Premixed Calibration Standards

» Documents


  • 80-8060H-PREMIX:
  • 80-8061-HGHM5:
  • 80-8062-HGUM5:

Product Highlights

  • Reference materials for targeted bisulfite NGS (tNGBS), EPIC Array, Pyrosequencing, and MS-HRM.
  • Tested on +14,000 gene specific and global methylation assays.
  • Control genomic DNA requires bisulfite conversion prior to use.

Product Information

Item No. Description Price Inquire
80-8060 Custom made DNA controls:  Low or high mentholated DNA, 5µg yield.  $632.50 Inquire
80-8060H-bsMix Human bisulfite modified genomic DNA  controls including 15 ul of each low, medium, and high methylated DNAs  $591.77 Inquire
80-8060H-PreMix Human Pre-Mixed  Methylation Controls at different ratios:
Low methylated DNA (0%), 10%, 25%, 50%, 75%, and high methylated DNA (100%).
 $382.82 Inquire
80-8060M-PreMix Moue Pre-Mixed Methylation Controls at different ratios:
Low methylated DNA (0%), 10%, 25%, 50%, 75%, and high methylated DNA (100%).
 $389.30 Inquire
80-8060PM-PreMix Monkey Pre-Mixed Methylation Controls at different ratios:
Low methylated DNA (0%), 10%, 25%, 50%, 75%, and high methylated DNA (100%).
$409.46 Inquire
80-8060R-PreMix Rat Pre-Mixed Methylation Controls at different ratios:
Low methylated DNA (0%), 10%, 25%, 50%, 75%, and high methylated DNA (100%).
 $389.30 Inquire
80-8061-HGHM5 Human: High Methylated Genomic DNA (5 µg at 100 ng/ µL)  $237.92 Inquire
80-8062-HGUM5 Human: Low Methylated Genomic DNA (5 µg at 100 ng/ µL)  $237.92 Inquire
80-8063-MGHM5 Mouse: High Methylated Genomic DNA (5 µg at 100 ng/ µL)  $248.73 Inquire
80-8064-MGUM5 Mouse: Low Methylated Genomic DNA (5 µg at 100 ng/ µL)  $248.73 Inquire
80-8065-RGHM5 Rat: High Methylated Genomic DNA (5 µg at 100 ng/ µL)  $248.73 Inquire
80-8066-RGUM5 Rat: Low Methylated Genomic DNA (5 µg at 100 ng/ µL)  $248.73 Inquire
80-8067-PMGHM5 Monkey (Rhesus): High Methylated Genomic DNA (5 µg at 100 ng/ µL)  $275.63 Inquire
80-8068-PMGUM5 Monkey (Rhesus): Low Methylated Genomic DNA (5 µg at 100 ng/ µL)  $275.63 Inquire
80-8069-LHM5 Bacteriophage Lambda: High Methylated Genomic DNA (5 µg at 100 ng/ µL)  $200.12 Inquire
80-8070-LLM5 Low Methylation Controls for LUMA Analysis  $200.12 Inquire
80-8081-HGMM5 Human: Medium Methylation DNA Genomic DNA  $297.40 Inquire
80-8082-MGMM5 Mouse: Medium Methylation DNA Genomic DNA  $310.92 Inquire
80-8083-RGMM5 Rat: Medium Methylation DNA Genomic DNA  $310.92 Inquire
80-8084-PMGMM5 Monkey: Medium Methylation DNA Genomic DNA  $344.54 Inquire
80-8090 Custom made pre-mixed methylation at different ratios:
Low methylated DNA (0%), 10%, 25%, 50%, 75%, and high methylated DNA (100%).
 $782.93 Inquire

Methylation Control Data

Targeted Bisulfite NGS (tNGBS) Results

Fig. 1a: Methylation levels in low methylated DNA using mouse Line-1 Pyrosequencing methylation assay.
low methylated control chart

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Pyrosequencing (tNGBS) Data

Fig. 1b: Mouse Cd274 methylation results using mouse Foxp3 Methylation Panel (N4V1P17) in mouse methylation controls as reference materials.
PCR Bias Testing Results

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MS-HRM Assay Validation Data

Fig. 1c: Human FOXP3 TSDR MS-HRM Assay validation using human methylation calibration standards
MS-HRM_data table

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HRM standard curve data chart

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Fig. 1d: Human Methylation QC using human BRCA promoter methylation assay
BRCA1 Pyrosequencing Methylation Testing Results

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Methylation Control Applications

Methylation control DNAs are useful for ensuring quality assay results in epigenetic studies.  They can be used in various DNA methylation analysis methods to ensure the assay in use provides quality data from unknown samples.  Bisulfite conversion techniques, bisulfite sequencing, MS-HRM, Infinium Methylation EPIC Array, methyl-DNA immunoprecipitation (Me-DIP), methyl-CpG binding domain-based (MBDCap) proteins, methylation-specific PCR (MSP), and real-time PCR are all methods in which these methylation controls could be utilized.

Custom panel design by EpigenDx

Experts Since 2006

Custom Panel Design

With over 15 years of experience, EpigenDx offers customizable DNA Methylation analysis for specific gene targets of your interest. We offer rapid turnaround time for clinical trials and molecular diagnosis as well as MGMT/Line-1/Foxp3 tests for HRM realtime PCR, Pyrosequencing, and targeted bisulfite NGS. Simply send us custom target regions with your genes of interest. We will design and validate a panel of assays suited to your research interests.

Quantitative Methodology Is Critical

Quantitative methodology is critical for assessing DNA methylation. The identification of appropriate promoter regions or key CpG dinucleotides that influence transcription for individual genes is also important The human genome contains ∼30,000 CpG islands (CGIs), long stretches (0.5–2 kb) of DNA with unusually elevated levels of CpG dinucleotides. In mammalian genomes, DNA methylation occurs at CpG dinucleotides and is a dynamic epigenetic control mechanism. At these locations, methylated CpG dinucleotides can cause a high rate of C to T substitution. It is well known that methylated CpG sites have a high mutation rate.

MS-HRM (Methylation-Sensitive High Resolution Melting) is a PCR-based in-tube approach for detecting methylation levels at specific loci. The assays have a high sensitivity, allowing detection of 0.1-1% methylation alleles in an unmethylated background, thanks to a novel primer design. MS-HRM primers are designed to complement the methylated allele, and a specific annealing temperature allows these primers to anneal to both the methylated and unmethylated alleles, increasing the assay’s sensitivity.

Quantitative Methodology by EpigenDx
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