ArticlePloS one2013
Quality evaluation of methyl binding domain based kits for enrichment DNA-methylation sequencing.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers, 1 of them a synthesis that pooled it.
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Who cites it
41 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Early diagnosis of ovarian cancer based on methylation profiles in peripheral blood cell-free DNA: a systematic review.Clinical epigenetics · 2023Pooled it
- Exploratory analysis of the human breast DNA methylation profile upon soymilk exposure.Scientific reports · 2018Trial
- Dynamic epigenetic changes to VHL occur with sunitinib in metastatic clear cell renal cancer.Oncotarget · 2016Trial
- DNA methylation in breast cancer: early detection and biomarker discovery through current and emerging approaches.Journal of translational medicine · 2025Review
- Human VDAC pseudogenes: an emerging role for VDAC1P8 pseudogene in acute myeloid leukemia.Biological research · 2023Article
- Urogenital pathogens in urine samples of clinically diagnosed urinary tract infected patients in Tanzania: A laboratory based cross-sectional study.IJID regions · 2023Article
- Evolved DNA Duplex Readers for Strand-Asymmetrically Modified 5-Hydroxymethylcytosine/5-Methylcytosine CpG Dyads.Journal of the American Chemical Society · 2022Article
- An Intelligent Classification System for Cancer Detection Based on DNA Methylation Using ML and Semantic Knowledge in Healthcare.Computational intelligence and neuroscience · 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
- 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
- Article
- Profiling DNA methylation differences between inbred mouse strains on the Illumina Human Infinium MethylationEPIC microarray.PloS one · 2018Article
- Comparative analysis of MBD-seq and MeDIP-seq and estimation of gene expression changes in a rodent model of schizophrenia.Genomics · 2017Article
- Methylome analysis of extreme chemoresponsive patients identifies novel markers of platinum sensitivity in high-grade serous ovarian cancer.BMC medicine · 2017Article
- Enrichment methods provide a feasible approach to comprehensive and adequately powered investigations of the brain methylome.Nucleic acids research · 2017Article
- Comprehensive DNA Methylation Analysis Using a Methyl-CpG-binding Domain Capture-based Method in Chronic Lymphocytic Leukemia Patients.Journal of visualized experiments : JoVE · 2017Article
- Epigenetic sampling effects: nephrectomy modifies the clear cell renal cell cancer methylome.Cellular oncology (Dordrecht, Netherlands) · 2017Article
- Conserved effect of aging on DNA methylation and association with EZH2 polycomb protein in mice and humans.Mechanisms of ageing and development · 2017Article
- Methyl-CpG/MBD2 Interaction Requires Minimum Separation and Exhibits Minimal Sequence Specificity.Biophysical journal · 2016Article
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA-methylation is an important epigenetic feature in health and disease. Methylated sequence capturing by Methyl Binding Domain (MBD) based enrichment followed by second-generation sequencing provides the best combination of sensitivity and cost-efficiency for genome-wide DNA-methylation profiling. However, existing implementations are numerous, and quality control and optimization require expensive external validation. Therefore, this study has two aims: 1) to identify a best performing kit for MBD-based enrichment using independent validation data, and 2) to evaluate whether quality evaluation can also be performed solely based on the characteristics of the generated sequences. Five commercially available kits for MBD enrichment were combined with Illumina GAIIx sequencing for three cell lines (HCT15, DU145, PC3). Reduced representation bisulfite sequencing data (all three cell lines) and publicly available Illumina Infinium BeadChip data (DU145 and PC3) were used for benchmarking. Consistent large-scale differences in yield, sensitivity and specificity between the different kits could be identified, with Diagenode's MethylCap kit as overall best performing kit under the tested conditions. This kit could also be identified with the Fragment CpG-plot, which summarizes the CpG content of the captured fragments, implying that the latter can be used as a tool to monitor data quality. In conclusion, there are major quality differences between kits for MBD-based capturing of methylated DNA, with the MethylCap kit performing best under the used settings. The Fragment CpG-plot is able to monitor data quality based on inherent sequence data characteristics, and is therefore a cost-efficient tool for experimental optimization, but also to monitor quality throughout routine applications.
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