A Comparison of Cell-Free DNA Isolation Kits

Abstract

The analysis of cell-free DNA (cfDNA) as a sensitive biomarker for cancer diagnosis and monitoring has resulted in a need for efficient and standardized cfDNA isolation. In this study, we compared the isolation efficiency of the QIAamp circulating nucleic acid kit (QIA) with four other cfDNA isolation kits: the PME free-circulating DNA Extraction Kit (PME), the Maxwell RSC ccfDNA Plasma Kit (RSC), the EpiQuick Circulating Cell-Free DNA Isolation Kit (EQ), and two consecutive versions of the NEXTprep-Mag cfDNA Isolation Kit (NpM). cfDNA was isolated from 10 plasma samples, of which five contained KRAS mutated cell-free tumor DNA (ctDNA). Digital droplet PCR was used to quantify the total cfDNA concentration as well as the KRAS mutated ctDNA fraction. cfDNA integrity was assessed with real-time quantitative PCR. The QIA and the RSC kits displayed similar isolation efficiencies of both KRAS mutated ctDNA and nonmutated cfDNA, whereas the yield generated by the PME and NpM kits was significantly lower. Real-time quantitative PCR indicated the presence of digital droplet PCR inhibiting agents in the eluates of the NpM and EQ kits. To conclude, this study presents two highly efficient isolation kits for cfDNA isolation, of which the RSC kit has the advantage of a fully automated protocol over the labor-intensive QIA kit.

Comparison of Four Commercial Kits for Isolation of Urinary Cell-Free DNA and Sample Storage Conditions

“…We summarize the characteristics of each kit in Table 1. QC specializes in cfDNA extraction, and many researchers have reported its efficient purification performance [17][18][19]. The QC has also been widely used for liquid biopsy using urinary cfDNA in various urologic and non-urologic malignancies [5,[28][29][30].…”

“…In addition, urinary cfDNA also reflects the systemic status of patients, as it is derived from both the urinary tract and the circulatory system [16]. However, although many studies have compared the various extraction methods of circulating cfDNA in blood [17][18][19], limited data are available on methods for urinary cfDNA extraction [20,21]. Most studies have been conducted on urinary DNA, regardless of being genomic DNA or cfDNA [22][23][24].…”

A DNA-modified hydrogel for simultaneous purification, concentration and detection of targeted cfDNA in human serum

“…19,20 There are many cfDNA isolation kits such as QIAamp circulating nucleic acid kit (QIA, Qiagen, Antwerp, Belgium), PME free-circulating DNA Extraction Kit (PME, Westburg, Leusden, The Netherlands), Maxwell RSC ccfDNA Plasma Kit (RSC, Promega, Leiden, The Netherlands), and EpiQuik Circulating Cell-Free DNA Isolation Kit (EQ, Epi-Gentek, Farmingdale, NY). 21,22 The commercial kits are extremely expensive and ineffective in specically separating the targeted DNA. Therefore, we aimed to construct a device for cfDNA isolation, with high sensitivity for low-concentration isolations and high specicity for fragment size-specic isolations.…”

Evaluation of five cell-free DNA isolation kits for plasma

“…A series of reports compared the homemade or commercially available cfDNA extraction kits [13][14][15][16][17][18], which gave valuable guidelines to select the suitable kits for different samples. Still there are limitations in these studies.…”