Year-end Sale % OFF 
Abstract
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.
Highlights
Epigenetic mechanisms such as DNA methylation and histone modifications have important roles in human biology and diseases
The choice of extraction methods was based on procedures previously used for in-house biobanking, and rely upon three different principles frequently applied in commercial kits and custom protocols
DNA was extracted from each donor applying three different extraction methods: 1) automatic extraction with a magnetic beadbased procedure on MagNA Pure LC (Roche Diagnostics), 2) automatic extraction with salting-out and isopropanol precipitation on Autopure LS (Qiagen), and 3) manual organic extraction followed by ethanol precipitation
Summary
Epigenetic mechanisms such as DNA methylation and histone modifications have important roles in human biology and diseases (e.g. cell differentiation [1], x-inactivation [2;3] and gene expression [4;5]). DNA methylation is the most widely studied epigenetic modification in humans, and Epigenome-wide association studies (EWAS). The method used to extract DNA often differs across samples in a study, reflecting e.g. different tissue types, different laboratories involved or changes in procedures over time. The aim of the present study was to determine whether three different DNA extraction methods (automatic extractions on MagNA Pure LC and Autopure LS, and manual organic extraction) could influence Infinium 450K DNA methylation values in whole blood. The choice of extraction methods was based on procedures previously used for in-house biobanking, and rely upon three different principles frequently applied in commercial kits and custom protocols (magnetic beads, salting-out followed by isopropanol precipitation, and organic extraction)
Sign-in/Register to view highlights & summary 
Published Version (
Free)
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
