ArticleGenome research2018
Whole-genome bisulfite sequencing with improved accuracy and cost.
Article in Genome research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 papers.
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
63 citing papers in PubMed, 124 citations in OpenAlex.
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- Advancements in DNA methylation technologies and their application in cancer diagnosis.Epigenetics · 2025Review
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- The 3PM transformation potential of minimal residual disease in solid tumor management: a bibliometric analysis and review.The EPMA journal · 2025Review
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- Complete reference genome and pangenome improve genome-wide detection and interpretation of DNA methylation using sequencing and array data.Cell reports · 2025Article
- Artificial Intelligence in cancer epigenomics: a review on advances in pan-cancer detection and precision medicine.Epigenetics & chromatin · 2025Review
- Evaluation of Illumina and Oxford Nanopore Sequencing for the Study of DNA Methylation in Alzheimer's Disease and Frontotemporal Dementia.International journal of molecular sciences · 2025Review
- Strengthening Rigor and Reproducibility in Epigenome-Wide Association Studies of Social Exposures and Brain-Based Health Outcomes.Current environmental health reports · 2025Review
- Reporting a Homozygous Case of Neurodevelopmental Disorder Associated With a Novel PRPF8 Variant.Molecular genetics & genomic medicine · 2025Article
- Fast and efficient method for parallel construction of targeted exome and methylome single-stranded DNA sequencing libraries.Scientific reports · 2025Article
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- Epigenetic Clocks: Beyond Biological Age, Using the Past to Predict the Present and Future.Aging and disease · 2024Review
- A review on trends in development and translation of omics signatures in cancer.Computational and structural biotechnology journal · 2024Review
- Epigenetic regulation of cardiovascular diseases induced by behavioral and environmental risk factors: Mechanistic, diagnostic, and therapeutic insights.FASEB bioAdvances · 2024Review
- DNA Methylation Patterns Associated with Tinnitus in Young Adults-A Pilot Study.Journal of the Association for Research in Otolaryngology : JARO · 2024Article
- Comparative DNA methylation reveals epigenetic adaptation to high altitude in snub-nosed monkeys.Zoological research · 2024Article
3 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors at 2 institutions in 1 country.
Funding
Abstract
DNA methylation patterns in the genome both reflect and help to mediate transcriptional regulatory processes. The digital nature of DNA methylation, present or absent on each allele, makes this assay capable of quantifying events in subpopulations of cells, whereas genome-wide chromatin studies lack the same quantitative capacity. Testing DNA methylation throughout the genome is possible using whole-genome bisulfite sequencing (WGBS), but the high costs associated with the assay have made it impractical for studies involving more than limited numbers of samples. We have optimized a new transposase-based library preparation assay for the Illumina HiSeq X platform suitable for limited amounts of DNA and providing a major cost reduction for WGBS. By incorporating methylated cytosines during fragment end repair, we reveal an end-repair artifact affecting 1%-2% of reads that we can remove analytically. We show that the use of a high (G + C) content spike-in performs better than PhiX in terms of bisulfite sequencing quality. As expected, the loci with transposase-accessible chromatin are DNA hypomethylated and enriched in flanking regions by post-translational modifications of histones usually associated with positive effects on gene expression. Using these transposase-accessible loci to represent the
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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.