Evaluation of Extracted Circulating Cell free DNA Concentration by Standard Nucleospin Plasma XS (NS) Kit Protocol Compared to its Modified Protocol

1.1.Background: One of the earliest and most common processes for cell-free DNA analysis is its extraction. Our study was to analyze cell-free plasma DNA of prostate cancer (PCA) and of benign prostatic hyperplasia (BPH) patients. 1.2.Methods:We extracted circulating cell-free DNA (ccfDNA) from 24 patients’ plasma samples (14 PCA; 10 BPH) by NucleoSpin plasma XS (NS) Kit using the standard kit protocol alongside with a second protocol with some modifications. Subsequently, NanoDrop, PCR and Real-time-PCR were used to evaluate the concentrations of the obtained DNA, respectively. 1.3.Results: Concentrations of the extracted cell free DNA with our modified protocol was significantly higher compared to the same DNA samples which were extracted with the company protocol (p value<0.001). 1.4.Conclusion:We could increase the rate of cell free DNA recovery to a much significant amount which is beneficial for investigators who need to evaluate gene expression in blood rather than not accessible organs and tissues. We recommend the modified protocol for NucleoSpin plasma XS (NS) Kit while the original protocol could not result in appropriate recovery of blood cell free DNA.