ArticlePloS one2015
Evaluation of Methyl-Binding Domain Based Enrichment Approaches Revisited.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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The trial behind it
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Who cites it
20 citing papers in PubMed.
- Translation of Epigenetics in Cell-Free DNA Liquid Biopsy Technology and Precision Oncology.Current issues in molecular biology · 2024Review
- Epigenetic targets in B- and T-cell lymphomas: latest developments.Therapeutic advances in hematology · 2023Review
- Cell-free DNA methylome profiling by MBD-seq with ultra-low input.Epigenetics · 2022Article
- Current and Emerging Technologies for the Analysis of the Genome-Wide and Locus-Specific DNA Methylation Patterns.Advances in experimental medicine and biology · 2022Article
- Spatial Learning Is Associated with Antagonist Outcomes for DNA Methylation and DNA Hydroxymethylation in the Transcriptional Regulation of the Ryanodine Receptor 3.Neural plasticity · 2021Article
- A methylation study of long-term depression risk.Molecular psychiatry · 2020Article
- MBD-seq - realities of a misunderstood method for high-quality methylome-wide association studies.Epigenetics · 2020Article
- Vitamin BJournal of neuroinflammation · 2020Article
- Cell Type-Specific Methylome-wide Association Studies Implicate Neurotrophin and Innate Immune Signaling in Major Depressive Disorder.Biological psychiatry · 2020Article
- Independent Methylome-Wide Association Studies of Schizophrenia Detect Consistent Case-Control Differences.Schizophrenia bulletin · 2020Article
- A model of pulldown alignments from SssI-treated DNA improves DNA methylation prediction.BMC bioinformatics · 2019Article
- DNA Methylation Cancer Biomarkers: Translation to the Clinic.Frontiers in genetics · 2019Review
- A Whole Methylome Study of Ethanol Exposure in Brain and Blood: An Exploration of the Utility of Peripheral Blood as Proxy Tissue for Brain in Alcohol Methylation Studies.Alcoholism, clinical and experimental research · 2018Article
- Profiling DNA methylation differences between inbred mouse strains on the Illumina Human Infinium MethylationEPIC microarray.PloS one · 2018Article
- A MBD-seq protocol for large-scale methylome-wide studies with (very) low amounts of DNA.Epigenetics · 2017Article
- Enrichment methods provide a feasible approach to comprehensive and adequately powered investigations of the brain methylome.Nucleic acids research · 2017Article
- Conserved effect of aging on DNA methylation and association with EZH2 polycomb protein in mice and humans.Mechanisms of ageing and development · 2017Article
- Correcting for cell-type effects in DNA methylation studies: reference-based method outperforms latent variable approaches in empirical studies.Genome biology · 2017Article
- Methyl-CpG/MBD2 Interaction Requires Minimum Separation and Exhibits Minimal Sequence Specificity.Biophysical journal · 2016Article
- A Whole Methylome CpG-SNP Association Study of Psychosis in Blood and Brain Tissue.Schizophrenia bulletin · 2016Article
Corrections and comments
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Authors and funding
8 authors.
Funding
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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