A Comparison of Cell-Free DNA Isolation Kits

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Presentation transcript:

A Comparison of Cell-Free DNA Isolation Kits Laure Sorber, Karen Zwaenepoel, Vanessa Deschoolmeester, Geert Roeyen, Filip Lardon, Christian Rolfo, Patrick Pauwels The Journal of Molecular Diagnostics Volume 19, Issue 1, Pages 162-168 (January 2017) DOI: 10.1016/j.jmoldx.2016.09.009 Copyright © 2017 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 1 A: Comparison of four cell-free DNA (cfDNA) isolation methods with the amount of total cfDNA in copies/μL generated with the QIAamp circulating nucleic acid kit (QIA), PME free-circulating DNA Extraction Kit (PME), 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 (NpMV1/NpMV2). The high yields of samples 7 and 10, generated by the RSC and QIA kits, respectively, are significantly different from the yields generated by the other kits. This is most likely because of contamination of these samples by genomic DNA of the buffy coat. No signals were generated by the samples isolated by the EQ and NpMV1 kits. B: The percentage of KRAS mutated cell-free tumor DNA (ctDNA) in copies/μL. None of the samples isolated by the PME, EQ, and NpMV1 kit generated a signal. The Journal of Molecular Diagnostics 2017 19, 162-168DOI: (10.1016/j.jmoldx.2016.09.009) Copyright © 2017 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 2 Comparison of the average quantitation cycle (Cq) values of the 105-bp and 236-bp fragments generated by cell-free DNA isolated with the QIAamp circulating nucleic acid kit (QIA), PME free-circulating DNA Extraction Kit (PME) (P = 0.007 and P = 0.028, respectively), Maxwell RSC ccfDNA Plasma Kit (RSC) (P = 0.762 and P = 0.119, respectively), EpiQuick Circulating Cell-Free DNA Isolation Kit (EQ) (P < 0.001 and P < 0.001, respectively), and the first and second version of the NEXTprep-Mag cfDNA Isolation Kit, NpMV1 (P = 0.002 and P = 0.01, respectively) and NpMV2 (P = 0.008 and P = 0.002, respectively). The highly deviating average Cq values of the EQ kit are because of the fact that for each fragment only one sample generated a significant fluorescent signal. The samples are expected to differ from each other, because they can originate from patients with metastasized or early-stage disease or from patients with benign pancreatic cysts. Statistical analysis was performed using all samples. GAPDH, glyceraldehyde-3-phosphate dehydrogenase. The Journal of Molecular Diagnostics 2017 19, 162-168DOI: (10.1016/j.jmoldx.2016.09.009) Copyright © 2017 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions