Background: The amount and quality of plasma cell free DNA (cfDNA) changes in extreme physiological and pathological conditions. These changes could provide a basis for a novel prognostic biomarker in conditions as diverse as pregnancy, cancer, organ transplantation and septicaemia. Evaluation of current methods for cfDNA analysis is needed to identify the best practical approach to medical diagnostics.
Methods: Initially, cf DNA was extracted from plasma of nine patients with febrile illness using both QIAamp Circulating Nucleic Acid and QI Aamp Mini Blood DNA kits. CfDNA concentration was determined by β-globin qPCR using PerfeCta and AmpliTaq mixes. Subsequently, Qubit fluorimetric and gel-on-a-chip assays were used to analyse plasma cfDNA from 64 additional patients with suspected septicaemia and positive blood cultures.
Results: Determination of CfDNA concentration by β-globin gene qPCR using AmpliTaq mix was superior to the PerfeCta qPCR. Moreover, unlike PerfeCta AmpliTaq qPCR determined similar genome equivalent copy numbers in cfDNA isolated by either DNA extraction method. QIAamp Mini Blood kit and AmpliTaq qPCR were subsequently used in a larger prospective study for cfDNA solation and quantification, respectively. However, qPCR was less suited for the detection of high plasma cfDNA levels when compared to direct DNA measurement by Qubit (mean 22.23 ng/ mL vs. 61.38 ng/mL, respectively) despite good correlation between the two methods. The DNA microfluidic chip method was then used to determine cfDNA fragments sizes and their relative concentrations revealing a presence of nucleosome-sized DNA fragments that were in strongly positive correlation with total cfDNA. Furthermore, apoptotic DNA was identified as a major DNA component in plasma with high cfDNA content.
Conclusions: β-globin qPCR is more suited to detection of low plasma cfDNA concentrations, while the Qubit assay is a better choice for rapid identification of high plasma concentrations. Apoptosis is a major source of cfDNA in plasma with high cfDNA concentrations based on DNA chip analysis.