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Detection and Monitoring of Tumor Associated Circulating DNA in Patient Biofluids
Published on: June 8, 2019
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Somatic Mutation Detection in Tumor Tissue and Matched Cell-Free DNA Using PCR-Based Methods in Pancreatic Cancer
Hana Zavrtanik Čarni1,2, David Badovinac1,2, Tanja Blagus3
1Department of Abdominal Surgery, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia.
International Journal of Molecular Sciences
|September 13, 2025
Summary
Digital PCR (dPCR) offers enhanced sensitivity for detecting KRAS and TP53 mutations in pancreatic cancer liquid biopsies. This advanced molecular technique shows promise for assessing tumor burden in the preoperative setting.
Area of Science:
- Oncology
- Molecular Biology
- Genetics
Background:
- Somatic mutations in KRAS and TP53 are frequent in pancreatic ductal adenocarcinoma (PDAC).
- Detecting these mutations via PCR in tumor tissue and cell-free DNA (cfDNA) offers minimally invasive tumor burden assessment.
- Highly sensitive methods are crucial as circulating tumor DNA (ctDNA) can be <0.1% of cfDNA in resectable PDAC.
Purpose of the Study:
- To evaluate competitive allele-specific PCR (castPCR) and digital PCR (dPCR) for detecting somatic mutations.
- Assess mutation detection in tumor tissue, cfDNA, and extracellular vesicle-associated DNA (EV-DNA) from plasma.
- Determine the utility of these assays in the preoperative setting for PDAC.
Main Methods:
- Collected matched primary tumor and preoperative plasma samples from 50 PDAC patients undergoing resection.
- Used castPCR for KRAS, TP53, SMAD4, and CDKN2A mutation detection in tumor DNA.
- Employed dPCR for KRAS and TP53 mutation analysis in tumor DNA, cfDNA, and EV-DNA.
Main Results:
- dPCR demonstrated higher sensitivity than castPCR in tumor tissue for KRAS p.G12D (28.6% additional detection) and TP53 p.R273H (39.6% additional detection).
- dPCR detected KRAS p.G12D in 10.2% and TP53 p.R273H in 2.0% of cfDNA samples.
- Mutation detection in EV-DNA was limited by low DNA yield; dPCR showed greater sensitivity overall.
Conclusions:
- Both castPCR and dPCR are effective for tumor DNA analysis, with dPCR offering superior sensitivity.
- Somatic mutation detection from liquid biopsies using dPCR holds significant potential for preoperative assessment in PDAC.
- Further research into EV-DNA analysis may enhance liquid biopsy applications.
