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Exploring the influence from whole blood DNA extraction methods on Infinium 450K DNA methylation
Genome-wide DNA methylation studies are becoming increasingly important in unraveling the epigenetic basis of cell biology, aging and human conditions. The aim of the present study was to explore whether different methods for extracting DNA from whole blood can affect DNA methylation outcome, potent...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6291135/ https://www.ncbi.nlm.nih.gov/pubmed/30540848 http://dx.doi.org/10.1371/journal.pone.0208699 |
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author | Hjorthaug, Hanne Sagsveen Gervin, Kristina Mowinckel, Petter Munthe-Kaas, Monica Cheng |
author_facet | Hjorthaug, Hanne Sagsveen Gervin, Kristina Mowinckel, Petter Munthe-Kaas, Monica Cheng |
author_sort | Hjorthaug, Hanne Sagsveen |
collection | PubMed |
description | Genome-wide DNA methylation studies are becoming increasingly important in unraveling the epigenetic basis of cell biology, aging and human conditions. The aim of the present study was to explore whether different methods for extracting DNA from whole blood can affect DNA methylation outcome, potentially confounding DNA methylation studies. DNA was isolated from healthy blood donors (n = 10) using three different extraction methods (i.e. two automatic extractions methods based on magnetic beads or isopropanol precipitation, and manual organic extraction). DNA methylation was analyzed using the Infinium HumanMethylation450 Bead Chip (Infinium 450K) (n = 30 samples in total), which is a frequently used method in genome-wide DNA methylation analyses. Overall, the different extraction methods did not have a significant impact on the global DNA methylation patterns. However, DNA methylation differences between organic extraction and each of the automated methods were in general larger than differences between the two automated extraction methods. No CpG sites or regions reached genome-wide significance when testing for differential methylation between extraction methods. Although this study is based on a small sample, these results suggest that extraction method is unlikely to confound Infinium 450K methylation analysis in whole blood. |
format | Online Article Text |
id | pubmed-6291135 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-62911352018-12-28 Exploring the influence from whole blood DNA extraction methods on Infinium 450K DNA methylation Hjorthaug, Hanne Sagsveen Gervin, Kristina Mowinckel, Petter Munthe-Kaas, Monica Cheng PLoS One Research Article Genome-wide DNA methylation studies are becoming increasingly important in unraveling the epigenetic basis of cell biology, aging and human conditions. The aim of the present study was to explore whether different methods for extracting DNA from whole blood can affect DNA methylation outcome, potentially confounding DNA methylation studies. DNA was isolated from healthy blood donors (n = 10) using three different extraction methods (i.e. two automatic extractions methods based on magnetic beads or isopropanol precipitation, and manual organic extraction). DNA methylation was analyzed using the Infinium HumanMethylation450 Bead Chip (Infinium 450K) (n = 30 samples in total), which is a frequently used method in genome-wide DNA methylation analyses. Overall, the different extraction methods did not have a significant impact on the global DNA methylation patterns. However, DNA methylation differences between organic extraction and each of the automated methods were in general larger than differences between the two automated extraction methods. No CpG sites or regions reached genome-wide significance when testing for differential methylation between extraction methods. Although this study is based on a small sample, these results suggest that extraction method is unlikely to confound Infinium 450K methylation analysis in whole blood. Public Library of Science 2018-12-12 /pmc/articles/PMC6291135/ /pubmed/30540848 http://dx.doi.org/10.1371/journal.pone.0208699 Text en © 2018 Hjorthaug et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Hjorthaug, Hanne Sagsveen Gervin, Kristina Mowinckel, Petter Munthe-Kaas, Monica Cheng Exploring the influence from whole blood DNA extraction methods on Infinium 450K DNA methylation |
title | Exploring the influence from whole blood DNA extraction methods on Infinium 450K DNA methylation |
title_full | Exploring the influence from whole blood DNA extraction methods on Infinium 450K DNA methylation |
title_fullStr | Exploring the influence from whole blood DNA extraction methods on Infinium 450K DNA methylation |
title_full_unstemmed | Exploring the influence from whole blood DNA extraction methods on Infinium 450K DNA methylation |
title_short | Exploring the influence from whole blood DNA extraction methods on Infinium 450K DNA methylation |
title_sort | exploring the influence from whole blood dna extraction methods on infinium 450k dna methylation |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6291135/ https://www.ncbi.nlm.nih.gov/pubmed/30540848 http://dx.doi.org/10.1371/journal.pone.0208699 |
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