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oxBS-450K: A method for analysing hydroxymethylation using 450K BeadChips

Stewart, SK; Morris, TJ; Guilhamon, P; Bulstrode, H; Bachman, M; Balasubramanian, S; Beck, S; (2014) oxBS-450K: A method for analysing hydroxymethylation using 450K BeadChips. Methods , 72 pp. 9-15. 10.1016/j.ymeth.2014.08.009. Green open access

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Abstract

DNA methylation analysis has become an integral part of biomedical research. For high-throughput applications such as epigenome-wide association studies, the Infinium HumanMethylation450 (450K) BeadChip is currently the platform of choice. However, BeadChip processing relies on traditional bisulfite (BS) based protocols which cannot discriminate between 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC). Here, we report the adaptation of the recently developed oxidative bisulfite (oxBS) chemistry to specifically detect both 5mC and 5hmC in a single workflow using 450K BeadChips, termed oxBS-450K. Supported by validation using mass spectrometry and pyrosequencing, we demonstrate reproducible (R(2)>0.99) detection of 5hmC in human brain tissue using the optimised oxBS-450K protocol described here.

Type: Article
Title: oxBS-450K: A method for analysing hydroxymethylation using 450K BeadChips
Open access status: An open access version is available from UCL Discovery
DOI: 10.1016/j.ymeth.2014.08.009
Publisher version: http://dx.doi.org/10.1016/j.ymeth.2014.08.009
Language: English
Additional information: Copyright © 2014 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/3.0/).
Keywords: 450K BeadChip, Bisulfite conversion, DNA methylation, Epigenetics, Hydroxymethylation, Oxidation
UCL classification: UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Cancer Institute
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Cancer Institute > Research Department of Cancer Bio
URI: https://discovery.ucl.ac.uk/id/eprint/1447467
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