Bead-Based Isolation of Circulating Tumor DNA from Pancreatic Cancer Patients Enables High Fidelity Next Generation Sequencing

Sukirthini Balendran-Braun,1,* Markus Kieler,2,* Sandra Liebmann-Reindl,3 Matthias Unseld,2 Daniela Bianconi,2 Gerald W Prager,2 Berthold Streubel1,3 1Department of Pathology, Medical University of Vienna, Vienna, Austria; 2Department of Medicine I, Division of Oncology, Comprehensive Cancer Center, Medical University, Vienna, Austria; 3Core Facility Genomics, Medical University of Vienna, Vienna, Austria*These authors contributed equally to this workCorrespondence: Berthold Streubel; Gerald W. Prager Email berthold.streubel@meduniwien.ac.at; gerald.prager@meduniwien.ac.atIntroduction: Pancreatic ductal adenocarcinoma (PDAC) is one of the most aggressive cancers and poses a challenge to the treating clinician. With the emergence of genomic profiling technologies, circulating tumor DNA (ctDNA) is increasingly recognized as a versatile biomarker for risk stratification and disease monitoring. We aimed to compare two commercially available NGS panels in a cohort of patients with advanced PDAC undergoing palliative chemotherapy.Methods: CtDNA was isolated with a magnetic bead-based protocol from two consecutive blood samples before and during chemotherapy in 21 patients with PDAC. Mutations were assessed by using a panel covering 15 (GP15) or 50 (GP50) cancer-associated genes. Results were compared to tumor tissue (GP15), if available.Results: Isolation of ctDNA resulted in a high mean value of 1.9 ng/μL (total volume of ∼ 40 μL). Although the same number of patients were positive for at least one mutation (76%), the most commonly mutated oncogene in PDAC, KRAS, was detectable in an additional 25% of all patients with the GP15 panel due to a higher coverage. The genomic concordance rate between tissue DNA and ctDNA analyses was 65.22%.Discussion: Our study demonstrates the feasibility of an NGS-based approach for ctDNA analysis and underlines the importance of using a disease-specific panel with a sufficiently high coverage.Keywords: pancreatic ductal adenocarcinoma, PDAC, liquid biopsy, circulating tumor DNA, ctDNA, next generation sequencing, NGS, KRAS, TP5