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

Sabrina K Stewart; Tiffany J Morris; Paul Guilhamon; Harry Bulstrode; Martin Bachman; Shankar Balasubramanian; Stephan Beck

doi:10.1016/j.ymeth.2014.08.009

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

Sabrina K Stewart, Tiffany J Morris, Paul Guilhamon, Harry Bulstrode, Martin Bachman, Shankar Balasubramanian, Stephan Beck

Research output: Contribution to journal › Article › peer-review

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.

Original language	English
Pages (from-to)	9-15
Number of pages	7
Journal	Methods
Volume	72
DOIs	https://doi.org/10.1016/j.ymeth.2014.08.009
Publication status	Published - 15 Jan 2015

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title = "oxBS-450K: a method for analysing hydroxymethylation using 450K BeadChips",

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.",

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doi = "10.1016/j.ymeth.2014.08.009",

language = "English",

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T1 - oxBS-450K

T2 - a method for analysing hydroxymethylation using 450K BeadChips

AU - Stewart, Sabrina K

AU - Morris, Tiffany J

AU - Guilhamon, Paul

AU - Bulstrode, Harry

AU - Bachman, Martin

AU - Balasubramanian, Shankar

AU - Beck, Stephan

PY - 2015/1/15

Y1 - 2015/1/15

N2 - 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.

AB - 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.

U2 - 10.1016/j.ymeth.2014.08.009

DO - 10.1016/j.ymeth.2014.08.009

M3 - Article

C2 - 25175075

VL - 72

SP - 9

EP - 15

JO - Methods

JF - Methods

SN - 1046-2023

ER -

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

Abstract

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