Comparison of Circulating Cell-Free DNA Extraction Methods for Downstream Analysis in Cancer Patients
Abstract
:1. Introduction
2. Results
2.1. Selection of Plasma Samples from Cancer Patients
2.2. Quantitative Comparison of DNA Yield with Different ccfDNA Extraction Methods
2.3. CcfDNA Integrity and Mutation Detection Assessment
2.4. Comparing ccfDNA Extraction Kits Using High-Volume Citrate Plasma Samples
3. Discussion
4. Materials and Methods
4.1. Sample Collection and Processing
4.2. CcfDNA Extraction Techniques
4.3. Yield and Integrity Assessment of the Different ccfDNA Extraction Methods
4.4. Statistical Analyses
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Kit | Manufacturer | Method | Input Volume (mL) | Elution Volume (µL) | Execution |
---|---|---|---|---|---|
QIAamp Circulating Nucleic Acid Kit (CNA) | Qiagen | Silica-based | 1–4 (0.9–2) | 20–150 (47–92) | Manual |
Maxwell RSC ccfDNA Plasma Kit (RSC) | Promega | Magnetic beads | 0.2–1 (0.7–0.9) | 50 (50) | Automated |
Zymo Quick ccfDNA Serum & Plasma Kit (Z) | Zymo research (BaseClear) | Silica-based | <10 (0.8–0.9) | >50 (47) | Manual |
QIAamp MinElute ccfDNA midi kit (ME) | Qiagen | Magnetic beads | 4–10 (8) | 20–80 (47) | Manual |
Fragment Analyzer | β-Actin One-Tube 3-Size ddPCR | ||
---|---|---|---|
Kit | Ratio S/M | Ratio 137/420 bp | Ratio 137/1950 bp |
CNA | 1.81 (1.58–2.67) | 1.64 (1.54–1.95) | 6.56 (5.55–10.3) |
ME | 3.10 (2.37–3.76) * | 1.73 (1.48–1.89) | 8.00 (6.47–9.31) |
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Share and Cite
van der Leest, P.; Boonstra, P.A.; ter Elst, A.; van Kempen, L.C.; Tibbesma, M.; Koopmans, J.; Miedema, A.; Tamminga, M.; Groen, H.J.M.; Reyners, A.K.L.; et al. Comparison of Circulating Cell-Free DNA Extraction Methods for Downstream Analysis in Cancer Patients. Cancers 2020, 12, 1222. https://doi.org/10.3390/cancers12051222
van der Leest P, Boonstra PA, ter Elst A, van Kempen LC, Tibbesma M, Koopmans J, Miedema A, Tamminga M, Groen HJM, Reyners AKL, et al. Comparison of Circulating Cell-Free DNA Extraction Methods for Downstream Analysis in Cancer Patients. Cancers. 2020; 12(5):1222. https://doi.org/10.3390/cancers12051222
Chicago/Turabian Stylevan der Leest, Paul, Pieter A. Boonstra, Arja ter Elst, Léon C. van Kempen, Marco Tibbesma, Jill Koopmans, Anneke Miedema, Menno Tamminga, Harry J. M. Groen, Anna K. L. Reyners, and et al. 2020. "Comparison of Circulating Cell-Free DNA Extraction Methods for Downstream Analysis in Cancer Patients" Cancers 12, no. 5: 1222. https://doi.org/10.3390/cancers12051222