ArticleNucleic acids research2007
Recovery of bisulfite-converted genomic sequences in the methylation-sensitive QPCR.
Article in Nucleic acids research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers, 2 of them syntheses that pooled it.
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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
34 citing papers in PubMed, 2 syntheses or guidelines pooled it, 67 citations in OpenAlex.
- Early diagnosis of ovarian cancer based on methylation profiles in peripheral blood cell-free DNA: a systematic review.Clinical epigenetics · 2023Pooled it
- Guidelines for pre-analytical conditions for assessing the methylation of circulating cell-free DNA.Clinical epigenetics · 2021Pooled it
- Brain tumor detection based on transcription regulation features identified from public cerebrospinal fluid cell-free DNA sequencing data.Translational cancer research · 2026Article
- Single-stranded pre-methylated 5mC adapters uncover the methylation profile of plasma ultrashort Single-stranded cell-free DNA.Nucleic acids research · 2024Article
- An epigenetic toolbox for conservation biologists.Evolutionary applications · 2024Article
- DNA Methylation Analysis.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Typing of semen-containing mixtures using ARMS-based semen-specific CpG-InDel/STR markers.International journal of legal medicine · 2022Article
- i-Motif formation and spontaneous deletions in human cells.Nucleic acids research · 2022Article
- Generating Sequencing-Based DNA Methylation Maps from Low DNA Input Samples.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Evaluation of whole-genome DNA methylation sequencing library preparation protocols.Epigenetics & chromatin · 2021Article
- Quantitative Epigenetics: A New Avenue for Crop Improvement.Epigenomes · 2020Review
- An Internal Control for Evaluating Bisulfite Conversion in the Analysis of Short Stature Homeobox 2 Methylation in Lung Cancer.Asian Pacific journal of cancer prevention : APJCP · 2019Article
- Prediction of smoking by multiplex bisulfite PCR with long amplicons considering allele-specific effects on DNA methylation.Clinical epigenetics · 2018Article
- Simple and cost-effective laboratory methods to evaluate and validate cell-free DNA isolation.BMC research notes · 2018Article
- Cell-type-specific brain methylomes profiled via ultralow-input microfluidics.Nature biomedical engineering · 2018Article
- An optimized rapid bisulfite conversion method with high recovery of cell-free DNA.BMC molecular biology · 2017Article
- Comparative analysis of 12 different kits for bisulfite conversion of circulating cell-free DNA.Epigenetics · 2017Article
- Article
- MethylMeter(®): bisulfite-free quantitative and sensitive DNA methylation profiling and mutation detection in FFPE samples.Epigenomics · 2016Article
- DNA methylation biomarkers: cancer and beyond.Genes · 2014Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Many methods for the detection of genomic DNA methylation states have appeared. Currently, nearly all such methods employ bisulfite-mediated deamination of denatured DNA. While this treatment effectively deaminates cytosines to uracils, leaving most 5-methylcytosines intact, it also introduces abasic sites that generate a significant number of single-strand breaks in DNA. We have investigated the interplay of these two processes in order to determine their relative effects on the methylation-sensitive QPCR method. The extent of cleavage of the input DNA is significant and appears to be an increasing function of DNA concentration. Even so, the results suggest that only approximately 10% of a 62-nt target will be lost due to degradation and targets up to 131 nt will suffer only a 20% loss. More significant losses were found to occur during the subsequent removal of bisulfite and desulfonation steps that appear to be the result of size selectivity associated with matrix binding and elution required prior to QPCR in the most commonly used protocols. For biospecimens yielding <1 microg of DNA, these findings suggest that bisulfite treatment, in current implementations of MS-QPCR, result in low recoveries that preclude reliable analysis of DNA methylation patterns regardless of target size.
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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.