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oxBS-450K: a method for analysing hydroxymethylation using 450K BeadChips.

Research paper by Sabrina K SK Stewart, Tiffany J TJ Morris, Paul P Guilhamon, Harry H Bulstrode, Martin M Bachman, Shankar S Balasubramanian, Stephan S Beck

Indexed on: 02 Sep '14Published on: 02 Sep '14Published in: Methods



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.