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Genome-wide study of the effect of blood collection tubes on the cell-free DNA methylome
The methylation pattern of cfDNA, isolated from liquid biopsies, is gaining substantial interest for diagnosis and monitoring of diseases. We have evaluated the impact of type of blood collection tube and time delay between blood draw and plasma preparation on bisulphite-based cfDNA methylation prof...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Taylor & Francis
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8216177/ https://www.ncbi.nlm.nih.gov/pubmed/33074045 http://dx.doi.org/10.1080/15592294.2020.1827714 |
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author | Van Paemel, Ruben De Koker, Andries Caggiano, Christa Morlion, Annelien Mestdagh, Pieter De Wilde, Bram Vandesompele, Jo De Preter, Katleen |
author_facet | Van Paemel, Ruben De Koker, Andries Caggiano, Christa Morlion, Annelien Mestdagh, Pieter De Wilde, Bram Vandesompele, Jo De Preter, Katleen |
author_sort | Van Paemel, Ruben |
collection | PubMed |
description | The methylation pattern of cfDNA, isolated from liquid biopsies, is gaining substantial interest for diagnosis and monitoring of diseases. We have evaluated the impact of type of blood collection tube and time delay between blood draw and plasma preparation on bisulphite-based cfDNA methylation profiling. Fifteen tubes of blood were drawn from three healthy volunteer subjects (BD Vacutainer K2E EDTA spray tubes, Streck Cell-Free DNA BCT tubes, PAXgene Blood ccfDNA tubes, Roche Cell-Free DNA Collection tubes and Biomatrica LBgard blood tubes in triplicate). Samples were either immediately processed or stored at room temperature for 24 or 72 hours before plasma preparation. DNA fragment size was evaluated by capillary electrophoresis. Reduced representation bisulphite sequencing was performed on the cell-free DNA isolated from these plasma samples. We evaluated the impact of blood tube and time delay on several quality control metrics. All preservation tubes performed similar on the quality metrics that were evaluated. Furthermore, a considerable increase in cfDNA concentration and the fraction of it derived from NK cells was observed after a 72-hour time delay in EDTA tubes. The methylation pattern of cfDNA is robust and reproducible in between the different preservation tubes. EDTA tubes processed as soon as possible, preferably within 24 hours, are the most cost effective. If immediate processing is not possible, preservation tubes are valid alternatives. |
format | Online Article Text |
id | pubmed-8216177 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Taylor & Francis |
record_format | MEDLINE/PubMed |
spelling | pubmed-82161772021-07-06 Genome-wide study of the effect of blood collection tubes on the cell-free DNA methylome Van Paemel, Ruben De Koker, Andries Caggiano, Christa Morlion, Annelien Mestdagh, Pieter De Wilde, Bram Vandesompele, Jo De Preter, Katleen Epigenetics Research Paper The methylation pattern of cfDNA, isolated from liquid biopsies, is gaining substantial interest for diagnosis and monitoring of diseases. We have evaluated the impact of type of blood collection tube and time delay between blood draw and plasma preparation on bisulphite-based cfDNA methylation profiling. Fifteen tubes of blood were drawn from three healthy volunteer subjects (BD Vacutainer K2E EDTA spray tubes, Streck Cell-Free DNA BCT tubes, PAXgene Blood ccfDNA tubes, Roche Cell-Free DNA Collection tubes and Biomatrica LBgard blood tubes in triplicate). Samples were either immediately processed or stored at room temperature for 24 or 72 hours before plasma preparation. DNA fragment size was evaluated by capillary electrophoresis. Reduced representation bisulphite sequencing was performed on the cell-free DNA isolated from these plasma samples. We evaluated the impact of blood tube and time delay on several quality control metrics. All preservation tubes performed similar on the quality metrics that were evaluated. Furthermore, a considerable increase in cfDNA concentration and the fraction of it derived from NK cells was observed after a 72-hour time delay in EDTA tubes. The methylation pattern of cfDNA is robust and reproducible in between the different preservation tubes. EDTA tubes processed as soon as possible, preferably within 24 hours, are the most cost effective. If immediate processing is not possible, preservation tubes are valid alternatives. Taylor & Francis 2020-10-19 /pmc/articles/PMC8216177/ /pubmed/33074045 http://dx.doi.org/10.1080/15592294.2020.1827714 Text en © 2020 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group. https://creativecommons.org/licenses/by-nc-nd/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivatives License (http://creativecommons.org/licenses/by-nc-nd/4.0/ (https://creativecommons.org/licenses/by-nc-nd/4.0/) ), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited, and is not altered, transformed, or built upon in any way. |
spellingShingle | Research Paper Van Paemel, Ruben De Koker, Andries Caggiano, Christa Morlion, Annelien Mestdagh, Pieter De Wilde, Bram Vandesompele, Jo De Preter, Katleen Genome-wide study of the effect of blood collection tubes on the cell-free DNA methylome |
title | Genome-wide study of the effect of blood collection tubes on the cell-free DNA methylome |
title_full | Genome-wide study of the effect of blood collection tubes on the cell-free DNA methylome |
title_fullStr | Genome-wide study of the effect of blood collection tubes on the cell-free DNA methylome |
title_full_unstemmed | Genome-wide study of the effect of blood collection tubes on the cell-free DNA methylome |
title_short | Genome-wide study of the effect of blood collection tubes on the cell-free DNA methylome |
title_sort | genome-wide study of the effect of blood collection tubes on the cell-free dna methylome |
topic | Research Paper |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8216177/ https://www.ncbi.nlm.nih.gov/pubmed/33074045 http://dx.doi.org/10.1080/15592294.2020.1827714 |
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