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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...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Hindawi
2021
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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. |
format | Online Article Text |
id | pubmed-8285169 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Hindawi |
record_format | MEDLINE/PubMed |
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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