Evaluation of Methyl-Binding Domain Based Enrichment Approaches Revisited

TL;DR

This study compares two MBD-enrichment kits for DNA methylation analysis, finding MethylMiner to be more efficient and suitable for large-scale studies.

Contribution

The study directly compares MethylMiner and MethylCap, clarifying their performance for methylome-wide association studies.

Findings

MethylMiner shows better enrichment efficiency and lower background noise compared to MethylCap.

MethylMiner is more suitable for MWAS due to its ability to target regions with the majority of CpGs.

Bisulfite sequencing confirmed the methylation status detected by both kits.

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.

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