Comparison of methods for circulating cell-free DNA isolation using blood from cancer patients: impact on biomarker testing

Background: The implementation of liquid biopsy for biomarker testing and response to treatment monitoring in cancer patients would presumable increase laboratory throughput, requiring the development of automated methods for circulating free DNA (cfDNA) isolation. Methods: The present study compares the MagNA Pure Compact (MPC) Nucleic Acid Isolation Kit I and Maxwell ® RSC (MR) ccfDNA Plasma Kit and the later with QIAamp Circulating Nucleid Acid (QCNA) Kit using 57 plasma samples from cancer patients. cfDNA concentration was measured using the Qubit fluorometer. DNA fragments lengt were assessed using the Agilent 2100 Bioanalyzer. Circulating tumor DNA (ctDNA) was quantified by digital PCR (dPCR). Results: Firstly, we observed that MPC method significantly extracted less cfDNA than MR (P Conclusions: Methods for isolation of cfDNA can affect DNA yield and molecular weight fractions recovery. These observations should be taken into account for cfDNA analysis in routine clinical practice.