ArticleBMC genomics2024
Comparing methylation levels assayed in GC-rich regions with current and emerging methods.
Article in BMC genomics, 2024. 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 17 papers.
What it found
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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.
The trial behind it
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
17 citing papers in PubMed.
- Comparison of nanopore sequencing, MethylationEPIC array, and EM-Seq for DNA methylation detection.Computational biology and chemistry · 2026Article
- DNA methylation profiles of quail blood cells by whole-genome bisulfite and Oxford Nanopore sequencing.Scientific data · 2026Article
- Genome-wide and gene-specific DNA methylation across developmental stages in Pogonomyrmex californicus: A socially polymorphic ant.Insect molecular biology · 2026Article
- Liquid biopsy epigenetics: establishing a molecular profile based on cell-free DNA.Molecular oncology · 2026Review
- Circulating extracellular vesicle DNA (EV-DNA) and cell-free DNA in ovarian cancer: pathological relevance and diagnostic applications.Extracellular vesicles and circulating nucleic acids · 2026Review
- A Functional Approach to Testing Overall Effect of Interaction Between DNA Methylation and SNPs.Statistics in medicine · 2026Article
- Reproductive Dysfunction and Testicular Epigenetic Alterations in Male Rats with Experimental Amebiasis: Evaluation of SPATA6 Methylation and Therapeutic Outcomes.Acta parasitologica · 2025Article
- DNA methylation and machine learning: challenges and perspective toward enhanced clinical diagnostics.Clinical epigenetics · 2025Review
- Bioinformatics Strategies in Breast Cancer Research.Biomolecules · 2025Review
- The distinct roles of genome, methylation, transcription, and translation on protein expression in Arabidopsis thaliana resolve the Central Dogma's information flow.Genome biology · 2025Article
- Comparison of current methods for genome-wide DNA methylation profiling.Epigenetics & chromatin · 2025Article
- Cost-effective promoter methylation analysis via target long-read bisulfite sequencing: a case study in severe preterm birth.BMC medical genomics · 2025Article
- Sperm DNA methylation landscape and its links to male fertility in a non-model teleost using EM-seq.Heredity · 2025Article
- MitSorter: a standalone tool for accurate discrimination of mtDNA and NuMT ONT reads based on differential methylation.Bioinformatics advances · 2025Article
- Comparison of enzymatic and bisulfite-based methods for sequencing-based cell-free DNA methylation profiling.Frontiers in epigenetics and epigenomics · 2025Article
- Methylation profiling in neuropathological tumors diagnosis: a comprehensive review.Frontiers in oncology · 2025Review
- Next-generation DNA methylation sequencing: loci and regions differentially methylated in adolescents with chronic postsurgical pain.Neurobiology of pain (Cambridge, Mass.)Article
Corrections and comments
- Erratum issued
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA methylation is an epigenetic mechanism that regulates gene expression, and for mammals typically occurs on cytosines within CpG dinucleotides. A significant challenge for methylation detection methods is accurately measuring methylation levels within GC-rich regions such as gene promoters, as inaccuracies compromise downstream biological interpretation of the data. To address this challenge, we compared methylation levels assayed using four different Methods Enzymatic Methyl-seq (EM-seq), whole genome bisulphite sequencing (WGBS), Infinium arrays (Illumina MethylationEPIC, "EPIC"), and Oxford Nanopore Technologies nanopore sequencing (ONT) applied to human DNA. Overall, all methods produced comparable and consistent methylation readouts across the human genome. The flexibility offered by current gold standard WGBS in interrogating genome-wide cytosines is surpassed technically by both EM-seq and ONT, as their coverages and methylation readouts are less prone to GC bias. These advantages are tempered by increased laboratory time (EM-seq) and higher complexity (ONT). We further assess the strengths and weaknesses of each method, and provide recommendations in choosing the most appropriate methylation method for specific scientific questions or translational needs.
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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.