Document Type

Article

Original Publication Date

2015

Journal/Book/Conference Title

PLOS One

Volume

10

Issue

7

DOI of Original Publication

10.1371/journal.pone.0132205

Comments

Originally published at http://dx.doi.org/10.1371/journal.pone.0132205

Date of Submission

November 2015

Abstract

Methyl-binding domain (MBD) enrichment followed by deep sequencing (MBD-seq), is a robust and cost efficient approach for methylome-wide association studies (MWAS). MBD-seq has been demonstrated to be capable of identifying differentially methylated regions, detecting previously reported robust associations and producing findings that replicate with other technologies such as targeted pyrosequencing of bisulfite converted DNA. There are several kits commercially available that can be used for MBD enrichment. Our previous work has involved MethylMiner (Life Technologies, Foster City, CA, USA) that we chose after careful investigation of its properties. However, in a recent evaluation of five commercially available MBD-enrichment kits the performance of the MethylMiner was deemed poor. Given our positive experience with MethylMiner, we were surprised by this report. In an attempt to reproduce these findings we here have performed a direct comparison of MethylMiner with MethylCap (Diagenode Inc, Denville, NJ, USA), the best performing kit in that study. We find that both MethylMiner and MethylCap are two well performing MBD-enrichment kits. However, MethylMiner shows somewhat better enrichment efficiency and lower levels of background “noise”. In addition, for the purpose of MWAS where we want to investigate the majority of CpGs, we find MethylMiner to be superior as it allows tailoring the enrichment to the regions where most CpGs are located. Using targeted bisulfite sequencing we confirmed that sites where methylation was detected by either MethylMiner or by MethylCap indeed were methylated.

Rights

Copyright: © 2015 Aberg et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Is Part Of

VCU Human and Molecular Genetics Publications

journal.pone.0132205.s001.DOCX (28 kB)
Number of methylated sites detected.

journal.pone.0132205.s002.DOCX (28 kB)
Pyrosequencing assay design for sites detected by MethylMiner.

journal.pone.0132205.s003.DOCX (31 kB)
Pyrosequencing assay design for sites detected by MethylCap.

journal.pone.0132205.s004.DOCX (30 kB)
Methylation detected by MethylMiner for CpG density range 1–3.

journal.pone.0132205.s005.DOCX (27 kB)
Methylation detected by MethylCap for CpG density range 1–3.

journal.pone.0132205.s006.DOCX (27 kB)
Methylation detected by MethylCap for CpG density range 9–11.

journal.pone.0132205.s007.DOCX (28 kB)
Mouse reference genome.

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