ArticleNucleic acids research2008
Errors in the bisulfite conversion of DNA: modulating inappropriate- and failed-conversion frequencies.
Article in Nucleic acids research, 2008. 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 78 papers, 1 of them a synthesis that pooled it.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
78 citing papers in PubMed, 1 synthesis or guideline pooled it, 157 citations in OpenAlex.
- Guidelines for pre-analytical conditions for assessing the methylation of circulating cell-free DNA.Clinical epigenetics · 2021Pooled it
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- DNA methylation as a biomarker of prenatal exposures: current challenges and opportunities.Environmental epigenetics · 2026Review
- Review
- Ultra-mild bisulfite outperforms existing methods for 5-methylcytosine detection with low input DNA.Nature communications · 2025Article
- Genomics and Epigenomics Approaches for the Quantification of Circulating Tumor DNA in Liquid Biopsy: Relevance of a Multimodal Strategy.International journal of molecular sciences · 2025Review
- Cost-effective solutions for high-throughput enzymatic DNA methylation sequencing.PLoS genetics · 2025Article
- Best practices for methylome characterization in novel species: a case study in the microalgae Microchloropsis.Communications biology · 2025Article
- Genome-wide DNA methylation patterns in Daphnia magna are not significantly associated with age.Epigenetics & chromatin · 2025Article
- Highly Sensitive and Specific Lateral Flow Detection for DNA Methylation Based on GIaI-Mediated Specific-Terminal-Mediated Polymerase Chain Reaction.Micromachines · 2025Article
- Long-read metagenomic sequencing negates inferred loss of cytosine methylation in Myxosporea (Cnidaria: Myxozoa).GigaScience · 2025Article
- Beyond the base pairs: comparative genome-wide DNA methylation profiling across sequencing technologies.Briefings in bioinformatics · 2024Article
- Transcriptomic era of cancers in females: new epigenetic perspectives and therapeutic prospects.Frontiers in oncology · 2024Review
- Article
- Comparison of methylation estimates obtained via MinION nanopore sequencing and sanger bisulfite sequencing in the TRPA1 promoter region.BMC medical genomics · 2023Article
- A qPCR technology for direct quantification of methylation in untreated DNA.Nature communications · 2023Article
- Computational Methods for Single-cell DNA Methylome Analysis.Genomics, proteomics & bioinformatics · 2023Review
- Cadmium nitrate and DNA methylation in gastropods: comparison between ovotestis and hepatopancreas.PeerJ · 2023Article
- Circulating Cell-Free DNA-Based Methylation Pattern in Saliva for Early Diagnosis of Head and Neck Cancer.Cancers · 2022Review
18 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
Bisulfite treatment can be used to ascertain the methylation states of individual cytosines in DNA. Ideally, bisulfite treatment deaminates unmethylated cytosines to uracils, and leaves 5-methylcytosines unchanged. Two types of bisulfite-conversion error occur: inappropriate conversion of 5-methylcytosine to thymine, and failure to convert unmethylated cytosine to uracil. Conventional bisulfite treatment requires hours of exposure to low-molarity, low-temperature bisulfite ('LowMT') and, sometimes, thermal denaturation. An alternate, high-molarity, high-temperature ('HighMT') protocol has been reported to accelerate conversion and to reduce inappropriate conversion. We used molecular encoding to obtain validated, individual-molecule data on failed- and inappropriate-conversion frequencies for LowMT and HighMT treatments of both single-stranded and hairpin-linked oligonucleotides. After accounting for bisulfite-independent error, we found that: (i) inappropriate-conversion events accrue predominantly on molecules exposed to bisulfite after they have attained complete or near-complete conversion; (ii) the HighMT treatment is preferable because it yields greater homogeneity among sites and among molecules in conversion rates, and thus yields more reliable data; (iii) different durations of bisulfite treatment will yield data appropriate to address different experimental questions; and (iv) conversion errors can be used to assess the validity of methylation data collected without the benefit of molecular encoding.
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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.