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Optimization of Preanalytical Variables for cfDNA Processing and Detection of ctDNA in Archival Plasma Samples

DNA released from cells into the peripheral blood is known as cell-free DNA (cfDNA), representing a promising noninvasive source of biomarkers that could be utilized to manage Diffuse Large B-Cell Lymphoma (DLBCL), among other diseases. The procedure for purification and handling of cfDNA is not yet...

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Autores principales: Nesic, Marijana, Bødker, Julie S., Terp, Simone K., Dybkær, Karen
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Hindawi 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8285169/
https://www.ncbi.nlm.nih.gov/pubmed/34307658
http://dx.doi.org/10.1155/2021/5585148
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author Nesic, Marijana
Bødker, Julie S.
Terp, Simone K.
Dybkær, Karen
author_facet Nesic, Marijana
Bødker, Julie S.
Terp, Simone K.
Dybkær, Karen
author_sort Nesic, Marijana
collection PubMed
description DNA released from cells into the peripheral blood is known as cell-free DNA (cfDNA), representing a promising noninvasive source of biomarkers that could be utilized to manage Diffuse Large B-Cell Lymphoma (DLBCL), among other diseases. The procedure for purification and handling of cfDNA is not yet standardized, and various preanalytical variables may affect the yield and analysis of cfDNA, including the purification kits, blood collection tubes, and centrifugation regime. Therefore, we aimed to investigate the impact of these preanalytical variables on the yield of cfDNA by comparing three different purification kits DNeasy Blood & Tissue Kit (Qiagen), QIAamp Circulating Nucleic Acid Kit (Qiagen), and Quick-cfDNA Serum & Plasma Kit (Zymo Research). Two blood collection tubes (BCTs), EDTA-K2 and Cell-Free DNA (Streck), stored at four different time points before plasma was separated and cfDNA purified, were compared, and for EDTA tubes, two centrifugation regimes at 2000 × g and 3000 × g were tested. Additionally, we have tested the utility of long-term archival blood samples from DLBCL patients to detect circulating tumor DNA (ctDNA). We observed a higher cfDNA yield using the QIAamp Circulating Nucleic Acid Kit (Qiagen) purification kit, as well as a higher cfDNA yield when blood samples were collected in EDTA BCTs, with a centrifuge regime at 2000 × g. Moreover, ctDNA detection was feasible from archival plasma samples with a median storage time of nine years.
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spelling pubmed-82851692021-07-22 Optimization of Preanalytical Variables for cfDNA Processing and Detection of ctDNA in Archival Plasma Samples Nesic, Marijana Bødker, Julie S. Terp, Simone K. Dybkær, Karen Biomed Res Int Research Article DNA released from cells into the peripheral blood is known as cell-free DNA (cfDNA), representing a promising noninvasive source of biomarkers that could be utilized to manage Diffuse Large B-Cell Lymphoma (DLBCL), among other diseases. The procedure for purification and handling of cfDNA is not yet standardized, and various preanalytical variables may affect the yield and analysis of cfDNA, including the purification kits, blood collection tubes, and centrifugation regime. Therefore, we aimed to investigate the impact of these preanalytical variables on the yield of cfDNA by comparing three different purification kits DNeasy Blood & Tissue Kit (Qiagen), QIAamp Circulating Nucleic Acid Kit (Qiagen), and Quick-cfDNA Serum & Plasma Kit (Zymo Research). Two blood collection tubes (BCTs), EDTA-K2 and Cell-Free DNA (Streck), stored at four different time points before plasma was separated and cfDNA purified, were compared, and for EDTA tubes, two centrifugation regimes at 2000 × g and 3000 × g were tested. Additionally, we have tested the utility of long-term archival blood samples from DLBCL patients to detect circulating tumor DNA (ctDNA). We observed a higher cfDNA yield using the QIAamp Circulating Nucleic Acid Kit (Qiagen) purification kit, as well as a higher cfDNA yield when blood samples were collected in EDTA BCTs, with a centrifuge regime at 2000 × g. Moreover, ctDNA detection was feasible from archival plasma samples with a median storage time of nine years. Hindawi 2021-07-08 /pmc/articles/PMC8285169/ /pubmed/34307658 http://dx.doi.org/10.1155/2021/5585148 Text en Copyright © 2021 Marijana Nesic et al. https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Nesic, Marijana
Bødker, Julie S.
Terp, Simone K.
Dybkær, Karen
Optimization of Preanalytical Variables for cfDNA Processing and Detection of ctDNA in Archival Plasma Samples
title Optimization of Preanalytical Variables for cfDNA Processing and Detection of ctDNA in Archival Plasma Samples
title_full Optimization of Preanalytical Variables for cfDNA Processing and Detection of ctDNA in Archival Plasma Samples
title_fullStr Optimization of Preanalytical Variables for cfDNA Processing and Detection of ctDNA in Archival Plasma Samples
title_full_unstemmed Optimization of Preanalytical Variables for cfDNA Processing and Detection of ctDNA in Archival Plasma Samples
title_short Optimization of Preanalytical Variables for cfDNA Processing and Detection of ctDNA in Archival Plasma Samples
title_sort optimization of preanalytical variables for cfdna processing and detection of ctdna in archival plasma samples
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8285169/
https://www.ncbi.nlm.nih.gov/pubmed/34307658
http://dx.doi.org/10.1155/2021/5585148
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