Vol 5, No 2 (2020)
Original article
Published online: 2020-06-15

open access

Page views 1356
Article views/downloads 1048
Get Citation

Connect on Social Media

Connect on Social Media

A comparison of four commercial kits used for isolating circulating cell-free DNA: QuickGeneMINI8L (Kurabo), Maxwell RSC cfDNA Plasma Kit (Promega), cfKapture 21 Kit (MagBio), and QIAamp MinElute ccfDNA Kit (Qiagen)

Katarzyna Boguszewska-Byczkiewicz1, Dariusz Jarych2, Izabela Drożdż3, Hamed Hamed Al Huwaidi4, Izabela Zawlik56, Agnieszka Kołacińska17
Medical Research Journal 2020;5(2):92-99.

Abstract

A minimally-invasive alternative to surgical biopsies is a liquid biopsy (LB), a technique that has recently revolutionized the management of a number of tumors. One potential target biomarker of LB is cell-free DNA (cfDNA), which can act as a very sensitive indicator for certain tumors. Currently, clinical efforts are focused on increasing the quality of the cfDNA isolated for analysis. The present study compares the efficiency of isolation by four commercial kits: QuickGeneMINI8L (Kurabo), Maxwell RSC cfDNA Plasma Kit (Promega), cfKapture 21 Kit (MagBio), and QIAamp MinElute ccfDNA Kit (Qiagen). In each case, cfDNA was isolated from three plasma samples and one serum sample. Available method for the isolation give the ability to enrich optimal diagnostic quantity of cfDNA. cfDNA can be successfully separated using all investigated kits. The greatest efficiency was demonstrated by the QIAamp MinElute ccfDNA Kit (Qiagen) and cfKapture 21 (MagBio). Large amounts of cell-free DNA can be successfully isolated from small volumes of plasma.

Article available in PDF format

View PDF Download PDF file

References

  1. Ponti G, Manfredini M, Tomasi A. Non-blood sources of cell-free DNA for cancer molecular profiling in clinical pathology and oncology. Crit Rev Oncol Hematol. 2019; 141: 36–42.
  2. Mandel P, Métais P. Les acides nucléiques du plasma sanguin chez l’homme. C R Séances Soc Biol. 1948; 142: 241–243.
  3. Keup C, Benyaa K, Hauch S, et al. Targeted deep sequencing revealed variants in cell-free DNA of hormone receptor-positive metastatic breast cancer patients. Cell Mol Life Sci. 2020; 77(3): 497–509.
  4. Shaw JA, Guttery DS, Hills A, et al. Mutation Analysis of Cell-Free DNA and Single Circulating Tumor Cells in Metastatic Breast Cancer Patients with High Circulating Tumor Cell Counts. Clin Cancer Res. 2017; 23(1): 88–96.
  5. Quandt D, Dieter Zucht H, Amann A, et al. Implementing liquid biopsies into clinical decision making for cancer immunotherapy. Oncotarget. 2017; 8(29): 48507–48520.
  6. Kim C, Paik S. Gene-expression-based prognostic assays for breast cancer. Nat Rev Clin Oncol. 2010; 7(6): 340–347.
  7. Shirkavand A, Boroujeni ZN, Aleyasin SA. Examination of methylation changes of , , , and genes in peripheral blood DNA in breast cancer patients. Indian J Cancer. 2018; 55(4): 366–371.
  8. Ma F, Guan Y, Yi Z, et al. Assessing tumor heterogeneity using ctDNA to predict and monitor therapeutic response in metastatic breast cancer. Int J Cancer. 2020; 146(5): 1359–1368.
  9. Cristofanilli M, Pierga JY, Reuben J, et al. The clinical use of circulating tumor cells (CTCs) enumeration for staging of metastatic breast cancer (MBC): International expert consensus paper. Crit Rev Oncol Hematol. 2019; 134: 39–45.
  10. Li X, Ye M, Zhang W, et al. Liquid biopsy of circulating tumor DNA and biosensor applications. Biosens Bioelectron. 2019; 126: 596–607.
  11. Leon SA, Green A, Yaros MJ, et al. Radioimmunoassay for nanogram quantities of DNA. J Immunol Methods. 1975; 9(2): 157–164.
  12. Gedvilaitė V, Schveigert D, Cicėnas S. Cell-free DNA in non-small cell lung cancer. Acta Med Litu. 2017; 24(2): 138–144.
  13. Esposito A, Criscitiello C, Trapani D, et al. The Emerging Role of "Liquid Biopsies," Circulating Tumor Cells, and Circulating Cell-Free Tumor DNA in Lung Cancer Diagnosis and Identification of Resistance Mutations. Curr Oncol Rep. 2017; 19(1): 1.
  14. Lui YYN, Chik KW, Chiu RWK, et al. Predominant hematopoietic origin of cell-free DNA in plasma and serum after sex-mismatched bone marrow transplantation. Clin Chem. 2002; 48(3): 421–427.
  15. Zheng YWL, Chan KC, Sun H, et al. Nonhematopoietically derived DNA is shorter than hematopoietically derived DNA in plasma: a transplantation model. Clin Chem. 2012; 58(3): 549–558.
  16. Herbreteau G, Vallée A, Knol AC, et al. Quantitative monitoring of circulating tumor DNA predicts response of cutaneous metastatic melanoma to anti-PD1 immunotherapy. Oncotarget. 2018; 9(38): 25265–25276.
  17. Underhill HR, Kitzman JO, Hellwig S, et al. Fragment Length of Circulating Tumor DNA. PLoS Genet. 2016; 12(7): e1006162.
  18. Li Li, Zhang J, Jiang X, et al. Promising clinical application of ctDNA in evaluating immunotherapy efficacy. Am J Cancer Res. 2018; 8(10): 1947–1956.
  19. Mouliere F, Robert B, Arnau Peyrotte E, et al. High fragmentation characterizes tumour-derived circulating DNA. PLoS One. 2011; 6(9): e23418.
  20. Jahr S, Hentze H, Englisch S, et al. DNA fragments in the blood plasma of cancer patients: quantitations and evidence for their origin from apoptotic and necrotic cells. Cancer Res. 2001; 61(4): 1659–1665.
  21. Lapin M, Oltedal S, Tjensvoll K, et al. Fragment size and level of cell-free DNA provide prognostic information in patients with advanced pancreatic cancer. J Transl Med. 2018; 16(1): 300.
  22. Rack B, Schindlbeck C, Jückstock J, et al. SUCCESS Study Group. Circulating tumor cells predict survival in early average-to-high risk breast cancer patients. J Natl Cancer Inst. 2014; 106(5).
  23. Gray ES, Rizos H, Reid AL, et al. Circulating tumor DNA to monitor treatment response and detect acquired resistance in patients with metastatic melanoma. Oncotarget. 2015; 6(39): 42008–42018.
  24. Cavallone L, Aldamry M, Lafleur J, et al. A Study of Pre-Analytical Variables and Optimization of Extraction Method for Circulating Tumor DNA Measurements by Digital Droplet PCR. Cancer Epidemiol Biomarkers Prev. 2019; 28(5): 909–916.
  25. Elshimali YI, Khaddour H, Sarkissyan M, et al. The clinical utilization of circulating cell free DNA (CCFDNA) in blood of cancer patients. Int J Mol Sci. 2013; 14(9): 18925–18958.
  26. Kirsch C, Weickmann S, Schmidt B, et al. An improved method for the isolation of free-circulating plasma DNA and cell-free DNA from other body fluids. Ann N Y Acad Sci. 2008; 1137: 135–139.
  27. Oellerich M, Schütz E, Beck J, et al. Using circulating cell-free DNA to monitor personalized cancer therapy. Crit Rev Clin Lab Sci. 2017; 54(3): 205–218.
  28. Freidin MB, Freydina DV, Leung M, et al. Circulating tumor DNA outperforms circulating tumor cells for KRAS mutation detection in thoracic malignancies. Clin Chem. 2015; 61(10): 1299–1304.
  29. Dawson SJ, Tsui DWY, Murtaza M, et al. Analysis of circulating tumor DNA to monitor metastatic breast cancer. N Engl J Med. 2013; 368(13): 1199–1209.
  30. Fiala C, Diamandis EP. Utility of circulating tumor DNA in cancer diagnostics with emphasis on early detection. BMC Med. 2018; 16(1): 166.
  31. Fleischhacker M, Schmidt B, Weickmann S, et al. Methods for isolation of cell-free plasma DNA strongly affect DNA yield. Clin Chim Acta. 2011; 412(23-24): 2085–2088.