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Updated: Jun 13, 2026

Targeted DNA Methylation Analysis by Next-generation Sequencing

Targeted DNA Methylation Analysis by Next-generation Sequencing

Published on: February 24, 2015

Quantitative 1-step DNA methylation analysis with native genomic DNA as template.

Thomas von Kanel¹, Dominik Gerber, André Schaller

¹Division of Human Genetics, Department of Pediatrics, Inselspital, University of Bern, Bern, Switzerland. thomas.von_kaenel@alumni.unibe.ch

Clinical Chemistry

|May 18, 2010

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This study introduces a rapid, quantitative 1-step DNA methylation assay. The novel method simplifies analysis, reduces errors, and aids in diagnosing imprinting disorders like Prader-Willi syndrome.

Area of Science:

Molecular Biology
Epigenetics
Genetics

Background:

Current DNA methylation analysis involves complex, multi-step procedures.
Bisulfite conversion or methylation-sensitive endonucleases are standard but cumbersome methods.
A simplified, quantitative DNA methylation analysis is needed.

Purpose of the Study:

To develop a novel, quantitative 1-step DNA methylation assay.
To facilitate and expedite DNA methylation analysis.
To improve accuracy and reliability in methylation studies.

Main Methods:

Combines methylation-sensitive FastDigest(R) endonuclease digestion with quantitative real-time PCR (qPCR) in a single reaction.
Evaluates DNA methylation by comparing quantification cycles with and without endonuclease.

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Targeted DNA Methylation Analysis by Next-generation Sequencing

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Published on: February 24, 2015

DNA Methylation: Bisulphite Modification and Analysis

DNA Methylation: Bisulphite Modification and Analysis

Published on: October 21, 2011

Genome-Wide Analysis of DNA Methylation in Gastrointestinal Cancer

Genome-Wide Analysis of DNA Methylation in Gastrointestinal Cancer

Published on: September 18, 2020

Includes control reactions for artifact detection, correction, and copy number assessment.

Main Results:

Successfully diagnosed Prader-Willi syndrome and Angelman syndrome in 35 individuals by analyzing SNRPN promoter methylation and copy number.
Demonstrated significantly increased accuracy (P < 0.05) with low-quality DNA using a proposed correction model.
Enabled analysis of DNA samples with decreased digestibility, common in retrospective studies.

Conclusions:

The novel DNA methylation assay significantly reduces hands-on time and handling errors.
Methylation analyses can be completed within 90 minutes post-DNA extraction.
The assay's precision, reliability, and speed make it suitable for diagnostic and high-throughput applications.