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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...

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Autores principales: Hjorthaug, Hanne Sagsveen, Gervin, Kristina, Mowinckel, Petter, Munthe-Kaas, Monica Cheng
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2018
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.
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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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