ArticleGenome research2025
Assessing DNA methylation detection for primary human tissue using Nanopore sequencing.
Article in Genome research, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- HPRC2: A human pangenome reference with near-complete coverage of common genetic variation.bioRxiv : the preprint server for biology · 2026Article
- Comprehensive benchmarking of tools for nanopore-based detection of DNA methylation.Nature communications · 2026Article
- Genome-wide DNA methylation analysis in pigs using long-read sequencing unveils high-altitude adaptation and allele-specific regulation.BMC genomics · 2026Article
- Population-scale detection of methylation outliers from long-read genome sequencing.medRxiv : the preprint server for health sciences · 2026Article
- Long-read sequencing technologies and bioinformatics: a new perspective for decoding DNA methylation modifications.Journal of translational medicine · 2026Review
- MethyNano: supervised contrastive pretraining enables robust and generalizable methylation detection from nanopore sequencing.Bioinformatics (Oxford, England) · 2026Article
- Haplotype-resolved DNA methylation at theNPJ dementia · 2026Article
- Oxford Nanopore Sequencing in pediatric emergency infectious diseases: from rapid diagnosis to precision medicine.Frontiers in cellular and infection microbiology · 2026Review
- Long-Read epigenetic clocks identify improved brain aging predictions.bioRxiv : the preprint server for biology · 2025Article
- Computational analysis of DNA methylation from long-read sequencing.Nature reviews. Genetics · 2025Review
- NANOME: A Nextflow pipeline for haplotype-aware allele-specific consensus DNA methylation detection by nanopore long-read sequencing.bioRxiv : the preprint server for biology · 2025Article
- 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
- Evolution of genome-wide methylation profiling technologies.Genome research · 2025Review
- The ZFHX3 GGC Repeat Expansion Underlying Spinocerebellar Ataxia Type 4 has a Common Ancestral Founder.Movement disorders : official journal of the Movement Disorder Society · 2025Article
- Long-read sequencing of hundreds of diverse brains provides insight into the impact of structural variation on gene expression and DNA methylation.bioRxiv : the preprint server for biology · 2024Article
- The Research Progress of DNA Methylation in the Development and Function of the Porcine Placenta.International journal of molecular sciences · 2024Review
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12 authors.
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Abstract
DNA methylation most commonly occurs as 5-methylcytosine (5mC) in the human genome and has been associated with human diseases. Recent developments in single-molecule sequencing technologies (Oxford Nanopore Technologies [ONT] and Pacific Biosciences [PacBio]) have enabled readouts of long, native DNA molecules, including cytosine methylation. ONT recently upgraded their Nanopore sequencing chemistry and kits from the R9 to the R10 version, which yielded increased accuracy and sequencing throughput. However, the effects on methylation detection have not yet been documented. Here, we performed a series of computational analyses to characterize differences in Nanopore-based 5mC detection between the ONT R9 and R10 chemistries. We compared 5mC calls in R9 and R10 for three human genome data sets: a cell line, a frontal cortex brain sample, and a blood sample. We performed an in-depth analysis on CpG islands and homopolymer regions, and documented high concordance for methylation detection among sequencing technologies. The strongest correlation was observed between Nanopore R10 and Illumina bisulfite technologies for cell line-derived data sets. Subtle differences in methylation data sets between technologies can impact analysis tools such as differential methylation calling software. Our findings show that comparisons can be drawn between methylation data from different Nanopore chemistries using guided hypotheses. This work will facilitate comparison among Nanopore data cohorts derived using different chemistries from large-scale sequencing efforts, such as the NIH CARD Long Read Initiative.
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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.