ArticlePloS one2015
Bisulfite Conversion of DNA: Performance Comparison of Different Kits and Methylation Quantitation of Epigenetic Biomarkers that Have the Potential to Be Used in Non-Invasive Prenatal Testing.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to trial NCT06662591 (A Multi-Center Multi-Omics Approach for Investigating Genetic and Epigenetic Mechanisms in Autism Spectrum Disorder), which is not on this map. Cited by 43 papers, 1 of them a synthesis that pooled it.
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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.
A Multi-Center Multi-Omics Approach for Investigating Genetic and Epigenetic Mechanisms in Autism Spectrum Disorder
Who cites it
43 citing papers in PubMed, 1 synthesis or guideline pooled it, 97 citations in OpenAlex.
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- CpG dinucleotide methylation of the SPDEF gene as a blood-based epigenetic biomarker for prostate cancer diagnosis.BMC urology · 2025Article
- Comparative performance evaluation of bisulfite- and enzyme-based DNA conversion methods.Clinical epigenetics · 2025Article
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- Evaluation of silica spin‑column and magnetic bead formats for rapid DNA methylation analysis in clinical and point‑of‑care settings.Biomedical reports · 2024Article
- Development of a novel panel for blood identification based on blood-specific CpG-linked SNP markers.International journal of legal medicine · 2024Article
- Uncovering Forensic Evidence: A Path to Age Estimation through DNA Methylation.International journal of molecular sciences · 2024Review
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- Genome-wide methylation patterns from canine nanopore assemblies.G3 (Bethesda, Md.) · 2023Article
- Evaluation of commercial kits for isolation and bisulfite conversion of circulating cell-free tumor DNA from blood.Clinical epigenetics · 2023Article
- BiocMAP: a Bioconductor-friendly, GPU-accelerated pipeline for bisulfite-sequencing data.BMC bioinformatics · 2023Article
- A qPCR technology for direct quantification of methylation in untreated DNA.Nature communications · 2023Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
introductionEpigenetic alterations, including DNA methylation, play an important role in the regulation of gene expression. Several methods exist for evaluating DNA methylation, but bisulfite sequencing remains the gold standard by which base-pair resolution of CpG methylation is achieved. The challenge of the method is that the desired outcome (conversion of unmethylated cytosines) positively correlates with the undesired side effects (DNA degradation and inappropriate conversion), thus several commercial kits try to adjust a balance between the two. The aim of this study was to compare the performance of four bisulfite conversion kits [Premium Bisulfite kit (Diagenode), EpiTect Bisulfite kit (Qiagen), MethylEdge Bisulfite Conversion System (Promega) and BisulFlash DNA Modification kit (Epigentek)] regarding conversion efficiency, DNA degradation and conversion specificity.
methodsPerformance was tested by combining fully methylated and fully unmethylated λ-DNA controls in a series of spikes by means of Sanger sequencing (0%, 25%, 50% and 100% methylated spikes) and Next-Generation Sequencing (0%, 3%, 5%, 7%, 10%, 25%, 50% and 100% methylated spikes). We also studied the methylation status of two of our previously published differentially methylated regions (DMRs) at base resolution by using spikes of chorionic villus sample in whole blood.
resultsThe kits studied showed different but comparable results regarding DNA degradation, conversion efficiency and conversion specificity. However, the best performance was observed with the MethylEdge Bisulfite Conversion System (Promega) followed by the Premium Bisulfite kit (Diagenode). The DMRs, EP6 and EP10, were confirmed to be hypermethylated in the CVS and hypomethylated in whole blood.
conclusionOur findings indicate that the MethylEdge Bisulfite Conversion System (Promega) was shown to have the best performance among the kits. In addition, the methylation level of two of our DMRs, EP6 and EP10, was confirmed. Finally, we showed that bisulfite amplicon sequencing is a suitable approach for methylation analysis of targeted regions.
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