A simple silica based DNA isolation method for cell-free DNA analysis from liquid biopsy

Abstract

Abstract Objectives Cell-free DNA (cfDNA) is a promising biomarker for cancer diagnostics. Blood is used as a liquid biopsy material which transports many types of biological components such as protein, circulating tumor cells, cfDNA, and extracellular RNA molecules. In this study, the yield and purity of extracted DNA were compared of seven different in-house DNA isolation methods and two different commercial kits from human blood samples. Methods Different in-house methods, guanidine thiocyanate (GuSCN) with silica method, phenol-chloroform-isoamylalcohol method-1, phenol-chloroform-isoamylalcohol method-2, phenol-chloroform-isoamylalcohol with ammonium acetate method, sodium N-lauryl sarcosine with glycogen method, sodium acetate method, sodium chloride with silica method and two different commercial kits “Quick-cfDNA serum & plasma kit” and “plasma/serum cell-free circulating DNA purification mini kit” were used. After DNA isolation, methods were compared with real time PCR technique (qPCR) and spectrophotometric methods. Results The results showed that the newly modified GuSCN with silica method gave much higher purity and yield than any other analyzed in-house isolation methods and commercial kits that were used. Conclusions The GuSCN with silica method is simple to set up, easy to use, inexpensive and environmentally safe. The method would be an alternative method for cfDNA isolation from liquid biopsy samples.