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Updated: Feb 8, 2026

Droplet Digital TRAP ddTRAP: Adaptation of the Telomere Repeat Amplification Protocol to Droplet Digital Polymerase Chain Reaction
Published on: May 3, 2019
Identification and Quantification of Heterogeneously-methylated DNA Fragments Using Epiallele-sensitive Droplet
Mario Menschikowski1, Carsten Jandeck2, Markus Friedemann2
1Institute of Clinical Chemistry and Laboratory Medicine, University Hospital "Carl Gustav Carus", Technical University of Dresden, Dresden, Germany Mario.Menschikowski@uniklinikum-dresden.de.
Background/Aim:
DNA methylation plays an important role in the initiation and propagation of carcinogenesis; however, the role of heterogeneously methylated epialleles is currently not well studied, also due to the lack of sensitive, unbiased and high throughput methods. Here, a newly developed droplet digital PCR (ddPCR)-based method was evaluated regarding its ability to quantify such heterogeneously methylated epialleles with sufficient analytical sensitivity and specificity.
Materials And Methods:
Genomic DNA from blood leukocytes and bone marrow aspirate of an 8-year old male with B-cell acute lymphoblastic leukemia (B-ALL) and from normal and malignant prostate cell lines were analysed using ddPCR.
Results:
By using these DNA samples, the specificity of an applied set of fluorescence-labeled probes was demonstrated as a proof of concept.
Conclusion:
All individual heterogeneously-methylated epialleles were quantifiable by a set of fluorescence-labeled probes with complementary sequences to epialleles in a closed-tube and high-throughput manner. The new method named epiallele-sensitive droplet digital PCR (EAST-ddPCR) may give new insights in the generation and regulation of epialleles and may help in finding new biomarkers for the diagnosis of benign und malignant diseases.
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