ArticleNucleic acids research2007
A new method for accurate assessment of DNA quality after bisulfite treatment.
Article in Nucleic acids research, 2007. 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 52 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
52 citing papers in PubMed, 1 synthesis or guideline pooled it, 127 citations in OpenAlex.
- Guidelines for pre-analytical conditions for assessing the methylation of circulating cell-free DNA.Clinical epigenetics · 2021Pooled it
- CMA-Nano: A DNA Methylation Detection Method for Nanopore Sequencing Data Based on a Cross-Modal Attention Mechanism.ACS omega · 2026Article
- Establishment and Performance Evaluation of a Multiplexed TET2-APOBEC-Mediated cfDNA Methylation Detection Workflow Using qPCR and dPCR Readouts.Journal of personalized medicine · 2026Article
- Methylated circulating tumor DNA: technical challenges and clinical applications in non-small cell lung cancer patients-a narrative review.Translational lung cancer research · 2026Review
- LEMONmethyl-seq: Targeted long-read DNA methylation profiling reveals dynamics of CRISPR epigenome editing and endogenous DNA methylation patterns.bioRxiv : the preprint server for biology · 2026Article
- Single-cell multi-omics in cancer immunotherapy: from tumor heterogeneity to personalized precision treatment.Molecular cancer · 2025Review
- A procedure for DNA methylation assessment in osteoporosis-related gene promoters of umbilical cord blood: A study on the Prospective Epidemiological Research Studies in Iran (PERSIAN) birth cohort.BioImpacts : BI · 2025Article
- Review
- Prediction of methylation status using WGS data of plasma cfDNA for multi-cancer early detection (MCED).Clinical epigenetics · 2024Article
- Article
- Profiling Walnut Fungal Pathobiome Associated with Walnut Dieback Using Community-Targeted DNA Metabarcoding.Plants (Basel, Switzerland) · 2023Article
- Whole human genome 5'-mC methylation analysis using long read nanopore sequencing.Epigenetics · 2022Article
- Evaluation of site-specific methylation of the CMV promoter and its role in CHO cell productivity of a recombinant monoclonal antibody.Antibody therapeutics · 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
- Laboratory methods to decipher epigenetic signatures: a comparative review.Cellular & molecular biology letters · 2021Review
- Systematic benchmarking of tools for CpG methylation detection from nanopore sequencing.Nature communications · 2021Article
- A newborn screening pilot study using methylation-sensitive high resolution melting on dried blood spots to detect Prader-Willi and Angelman syndromes.Scientific reports · 2020Article
- HIF1α/TET1 Pathway Mediates Hypoxia-Induced Adipocytokine Promoter Hypomethylation in Human Adipocytes.Cells · 2020Article
- Article
- Methylation Changes of Primary Tumors, Monolayer, and Spheroid Tissue Culture Environments in Malignant Melanoma and Breast Carcinoma.BioMed research international · 2019Article
Corrections and comments
- Erratum issued
Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The covalent addition of methylgroups to cytosine has become the most intensively researched epigenetic DNA marker. The vast majority of technologies used for DNA methylation analysis rely on a chemical reaction, the so-called 'bisulfite treatment', which introduces methylation-dependent sequence changes through selective chemical conversion of non-methylated cytosine to uracil. After treatment, all non-methylated cytosine bases are converted to uracil but all methylated cytosine bases remain cytosine. These methylation dependent C-to-T changes can subsequently be studied using conventional DNA analysis technologies. The bisulfite conversion protocol is susceptible to processing errors, and small deviation from the protocol can result in failure of the treatment. Several attempts have been made to simplify the procedure and increase its robustness. Although significant achievements in this area have been made, bisulfite treatment remains the main source of process variability in the analysis of DNA methylation. This variability in particular impairs assays, which strive for the quantitative assessment of DNA methylation. Here we present basic mathematical considerations, which should be taken into account when analyzing DNA methylation. We also introduce a PCR-based assay, which allows ab initio assessment of the DNA quality after bisulfite treatment and can help to prevent inaccurate quantitative measurement resulting from poor bisulfite treatment.
Indexed as
Identifiers
What OpenQuestion holds
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.