ArticleGenome research2010
Evaluation of affinity-based genome-wide DNA methylation data: effects of CpG density, amplification bias, and copy number variation.
Article in Genome research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 74 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
74 citing papers in PubMed.
- DNA methylation marker to estimate the breast cancer cell fraction in DNA samples.Medical oncology (Northwood, London, England) · 2018Trial
- Exploratory analysis of the human breast DNA methylation profile upon soymilk exposure.Scientific reports · 2018Trial
- Amplification-free cancer diagnosis based on inhibition of Cas12a activity by site-specific 5mC-modified cfDNA.Nucleic acids research · 2025Article
- Review
- The Resistin/TLR4/miR-155-5p axis: a novel signaling pathway in the onset of hypothalamic neuroinflammation.Journal of neuroinflammation · 2025Article
- Hypermethylation at 45S rDNA promoter in cancers.PloS one · 2025Article
- Whole transcriptomic analysis reveals overexpression of salivary gland and cuticular proteins genes in insecticide-resistant Anopheles arabiensis from Western Kenya.BMC genomics · 2024Article
- Article
- The mitoepigenome responds to stress, suggesting novel mito-nuclear interactions in vertebrates.BMC genomics · 2023Article
- 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 metabolic labeling method detects mNature chemical biology · 2020Article
- The DNA hypermethylation phenotype of colorectal cancer liver metastases resembles that of the primary colorectal cancers.BMC cancer · 2020Article
- DOT1L complex suppresses transcription from enhancer elements and ectopic RNAi inRNA (New York, N.Y.) · 2019Article
- Article
- Interplay between small RNA pathways shapes chromatin landscapes in C. elegans.Nucleic acids research · 2019Article
- Article
- Intrauterine Programming of Diabetes Induced Cardiac Embryopathy.Diabetes & obesity international journal · 2019Article
- MeDEStrand: an improved method to infer genome-wide absolute methylation levels from DNA enrichment data.BMC bioinformatics · 2018Article
- DNA methylation patterns in peripheral blood mononuclear cells from Holstein cattle with variable milk yield.BMC genomics · 2018Article
- Modulation of mitochondrial DNA copy number in a model of glioblastoma induces changes to DNA methylation and gene expression of the nuclear genome in tumours.Epigenetics & chromatin · 2018Article
14 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA methylation is an essential epigenetic modification that plays a key role associated with the regulation of gene expression during differentiation, but in disease states such as cancer, the DNA methylation landscape is often deregulated. There are now numerous technologies available to interrogate the DNA methylation status of CpG sites in a targeted or genome-wide fashion, but each method, due to intrinsic biases, potentially interrogates different fractions of the genome. In this study, we compare the affinity-purification of methylated DNA between two popular genome-wide techniques, methylated DNA immunoprecipitation (MeDIP) and methyl-CpG binding domain-based capture (MBDCap), and show that each technique operates in a different domain of the CpG density landscape. We explored the effect of whole-genome amplification and illustrate that it can reduce sensitivity for detecting DNA methylation in GC-rich regions of the genome. By using MBDCap, we compare and contrast microarray- and sequencing-based readouts and highlight the impact that copy number variation (CNV) can make in differential comparisons of methylomes. These studies reveal that the analysis of DNA methylation data and genome coverage is highly dependent on the method employed, and consideration must be made in light of the GC content, the extent of DNA amplification, and the copy number.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.