Research Papers:

Identification of rare levels of methylated tumor DNA fragments using an optimized bias based pre-amplification-digital droplet PCR (OBBPA-ddPCR)

Mario Menschikowski _, Carsten Jandeck, Markus Friedemann, Brit Nacke, Saskia Hantsche, Oliver Tiebel, Olga Sukocheva and Albert Hagelgans

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Oncotarget. 2018; 9:36137-36150. https://doi.org/10.18632/oncotarget.26315

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Mario Menschikowski1, Carsten Jandeck1, Markus Friedemann1, Brit Nacke1, Saskia Hantsche1, Oliver Tiebel1, Olga Sukocheva2 and Albert Hagelgans1

1Institute of Clinical Chemistry and Laboratory Medicine, Carl Gustav Carus University Hospital, Technical University of Dresden, Dresden, Germany

2School of Health Sciences, Flinders University of South Australia, Adelaide, Australia

Correspondence to:

Mario Menschikowski, email: [email protected]

Keywords: liquid biopsy; free circulating DNA (fc-DNA); methylated DNA; tumor DNA; digital PCR

Received: June 30, 2018    Accepted: October 24, 2018    Published: November 16, 2018


Background: The analysis of aberrant DNA methylations is used for the diagnosis of cancer as significant changes in the gene methylation pattern are often detected during early carcinogenesis. In this study, we evaluated the performance of a two-step method that combines pre-amplification with ddPCR technique.

Results: By using ddPCR, the dependence of amplification efficiency for methylated and unmethylated DNA fragments on the relevant MgCl2 concentration and the annealing temperature was established in addition to the primer design. We found that the efficiency can be adjusted toward methylated sequences by using primers covering one to four CpG sites under appropriately selected MgCl2 concentration and annealing temperature. Applying a PCR bias between 85% and 95%, five copies of methylated tumor DNA fragments were detected against a background of 700,000 copies of unmethylated DNA fragments with a high signal-to-noise ratio. The analysis of serum samples from patients with prostate cancer showed a significantly improved performance of the new method in comparison with the MS-HRM technique, ddPCR alone, or ddPCR in combination with an unbiased pre-amplification using methylation-independent primers.

Conclusions: We define this method as an optimized bias-based pre-amplification-digital droplet PCR (OBBPA-ddPCR) technique. This novel method is recommended for the early detection of cancer-specific DNA methylation biomarkers in the form of a liquid biopsy.

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