ReviewEpigenetics & chromatin2015
Genome-wide assays that identify and quantify modified cytosines in human disease studies.
Review in Epigenetics & chromatin, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 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
24 citing papers in PubMed, 36 citations in OpenAlex.
- Comparative DNA methylation reveals epigenetic adaptation to high altitude in snub-nosed monkeys.Zoological research · 2024Article
- Benchmark of the Oxford Nanopore, EM-seq, and HumanMethylationEPIC BeadChip for the detection of the 5mC sites in cancer and normal samples.Frontiers in epigenetics and epigenomics · 2024Article
- DiseaseMeth version 3.0: a major expansion and update of the human disease methylation database.Nucleic acids research · 2022Article
- Ten Years of EWAS.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2021Review
- Candidate genes linking maternal nutrient exposure to offspring health via DNA methylation: a review of existing evidence in humans with specific focus on one-carbon metabolism.International journal of epidemiology · 2018Review
- Whole-genome bisulfite sequencing with improved accuracy and cost.Genome research · 2018Article
- Differential expression and methylation of integrin subunit alpha 11 and thrombospondin in the amnion of preterm birth.Obstetrics & gynecology science · 2018Article
- "Same difference": comprehensive evaluation of four DNA methylation measurement platforms.Epigenetics & chromatin · 2018Article
- Role of DNA methylation in altered gene expression patterns in adult zebrafish (Environmental epigenetics · 2018Article
- Associating cellular epigenetic models with human phenotypes.Nature reviews. Genetics · 2017Review
- Whole genome DNA methylation: beyond genes silencing.Oncotarget · 2017Review
- Empirical comparison of reduced representation bisulfite sequencing and Infinium BeadChip reproducibility and coverage of DNA methylation in humans.NPJ genomic medicine · 2017Article
- Article
- Novel epigenetic changes in CDKN2A are associated with progression of cervical intraepithelial neoplasia.Gynecologic oncology · 2016Article
- Transcriptomics in type 2 diabetes: Bridging the gap between genotype and phenotype.Genomics data · 2016Article
- 25-Hydroxyvitamin D in pregnancy and genome wide cord blood DNA methylation in two pregnancy cohorts (MoBa and ALSPAC).The Journal of steroid biochemistry and molecular biology · 2016Article
- Genetics of ankylosing spondylitis--insights into pathogenesis.Nature reviews. Rheumatology · 2016Review
- The Role of DNA Methylation in Cardiovascular Risk and Disease: Methodological Aspects, Study Design, and Data Analysis for Epidemiological Studies.Circulation research · 2016Review
- Amnion as a surrogate tissue reporter of the effects of maternal preeclampsia on the fetus.Clinical epigenetics · 2016Article
- DNA methylation: conducting the orchestra from exposure to phenotype?Clinical epigenetics · 2016Review
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The number of different assays that has been published to study DNA methylation is extensive, complemented by recently described assays that test modifications of cytosine other than the most abundant 5-methylcytosine (5mC) variant. In this review, we describe the considerations involved in choosing how to study 5mC throughout the genome, with an emphasis on the common application of testing for epigenetic dysregulation in human disease. While microarray studies of 5mC continue to be commonly used, these lack the additional qualitative information from sequencing-based approaches that is increasingly recognized to be valuable. When we test the representation of functional elements in the human genome by several current assay types, we find that no survey approach interrogates anything more than a small minority of the nonpromoter cis-regulatory sites where DNA methylation variability is now appreciated to influence gene expression and to be associated with human disease. However, whole-genome bisulphite sequencing (WGBS) adds a substantial representation of loci at which DNA methylation changes are unlikely to be occurring with transcriptional consequences. Our assessment is that the most effective approach to DNA methylation studies in human diseases is to use targeted bisulphite sequencing of the cis-regulatory loci in a cell type of interest, using a capture-based or comparable system, and that no single design of a survey approach will be suitable for all cell types.
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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.