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Open AccessArticle

Comparison of Circulating Cell-Free DNA Extraction Methods for Downstream Analysis in Cancer Patients

1
Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
2
Department of Medical Oncology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
3
Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
*
Author to whom correspondence should be addressed.
Both authors contributed equally.
Cancers 2020, 12(5), 1222; https://doi.org/10.3390/cancers12051222
Received: 3 April 2020 / Revised: 5 May 2020 / Accepted: 8 May 2020 / Published: 13 May 2020
(This article belongs to the Special Issue Liquid Biopsy: Latest Advances and Future Challenges)
Circulating cell-free DNA (ccfDNA) may contain DNA originating from the tumor in plasma of cancer patients (ctDNA) and enables noninvasive cancer diagnosis, treatment predictive testing, and response monitoring. A recent multicenter evaluation of workflows by the CANCER-ID consortium using artificial spiked-in plasma showed significant differences and consequently the importance of carefully selecting ccfDNA extraction methods. Here, the quantity and integrity of extracted ccfDNA from the plasma of cancer patients were assessed. Twenty-one cancer patient-derived cell-free plasma samples were selected to compare the Qiagen CNA, Maxwell RSC ccfDNA plasma, and Zymo manual quick ccfDNA kit. High-volume citrate plasma samples collected by diagnostic leukapheresis from six cancer patients were used to compare the Qiagen CNA (2 mL) and QIAamp MinElute ccfDNA kit (8 mL). This study revealed similar integrity and similar levels of amplified short-sized fragments and tumor-specific mutants comparing the CNA and RSC kits. However, the CNA kit consistently showed the highest yield of ccfDNA and short-sized fragments, while the RSC and ME kits showed higher variant allelic frequencies (VAFs). Our study pinpoints the importance of standardizing preanalytical conditions as well as consensus on defining the input of ccfDNA to accurately detect ctDNA and be able to compare results in a clinical routine practice, within and between clinical studies. View Full-Text
Keywords: ccfDNA; ctDNA; extraction; yield; integrity ccfDNA; ctDNA; extraction; yield; integrity
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MDPI and ACS Style

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.; Schuuring, E. Comparison of Circulating Cell-Free DNA Extraction Methods for Downstream Analysis in Cancer Patients. Cancers 2020, 12, 1222. https://doi.org/10.3390/cancers12051222

AMA Style

van der Leest P, Boonstra PA, ter Elst A, van Kempen LC, Tibbesma M, Koopmans J, Miedema A, Tamminga M, Groen HJM, Reyners AKL, Schuuring E. 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 Style

van der Leest, Paul; Boonstra, Pieter A.; ter Elst, Arja; van Kempen, Léon C.; Tibbesma, Marco; Koopmans, Jill; Miedema, Anneke; Tamminga, Menno; Groen, Harry J.M.; Reyners, Anna K.L.; Schuuring, Ed. 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

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