ArticleGenome biology2024
A comparison of methods for detecting DNA methylation from long-read sequencing of human genomes.
Article in Genome biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 76 papers, 1 of them a synthesis that pooled it.
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Who cites it
76 citing papers in PubMed, 1 synthesis or guideline pooled it, 79 citations in OpenAlex.
- Long-Read sequencing in psychiatric omics: a systematic review of current evidence.Molecular psychiatry · 2026Pooled it
- From epigenetic mark detection to rational design of epigenetic editing strategies.Molecular therapy. Advances · 2026Review
- Integrative Epigenomics: Bioinformatics Strategies for Multi-Omics Data Analysis in Health and Disease.Epigenomes · 2026Review
- DNA Methylation as a Programmable Information Layer: From Molecular Marks to Disease State Engineering.International journal of molecular sciences · 2026Review
- Nanopore sequencing identifies parent-of-origin specific age-associated methylation changes at imprinted loci in the human genome.Nature communications · 2026Article
- The Impact of Nutrition on DNA Methylation: Methodological Challenges in Understanding Cause and Effect.Nutrients · 2026Review
- Comprehensive benchmarking of tools for nanopore-based detection of DNA methylation.Nature communications · 2026Article
- CMA-Nano: A DNA Methylation Detection Method for Nanopore Sequencing Data Based on a Cross-Modal Attention Mechanism.ACS omega · 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
- MeDiCNet: Integrating Multi-scale Dynamic Convolution and Enhanced Position-Aware Transformer for DNA Methylation Site Prediction.Interdisciplinary sciences, computational life sciences · 2026Article
- Characterizing cytosine methylation of polymorphic transposable element insertions using the human pangenome resources.Genome research · 2026Article
- From Spatial Epigenomes to Clinical Diagnostics: Integrative Methylomics Across Scales and Modalities.International journal of molecular sciences · 2026Review
- Contrasting epigenetics of Ixodes scapularis populations.Scientific reports · 2026Article
- Long-read MitoScope reveals tissue-resolved somatic mitochondrial variation and landscape of nuclear-embedded mitochondrial sequences.bioRxiv : the preprint server for biology · 2026Article
- Mechanisms of DNA methyltransferase 3A1-mediated DNA methylation of nucleosomes.The Journal of biological chemistry · 2026Article
- Enhanced multicancer screening assay through whole-genome methylation sequencing-based multimodal cell-free DNA analysis.Experimental & molecular medicine · 2026Article
- Epigenetic Signatures of Ageing in Asian Elephants Revealed by Reduced Representation Bisulphite Sequencing.Evolutionary applications · 2026Article
- DNA Methylation Dynamics in Plant Abiotic Stress Response: Mechanisms, Memory, and Breeding Applications.Genes · 2026Review
- Methylation profile characteristics in the H19/IGF2:IG-DMR revealed by long-read sequencing analysis in patients with Beckwith-Wiedemann syndrome having defects in the OCT4/SOX2 binding site.Clinical epigenetics · 2026Article
16 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
13 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundLong-read sequencing can enable the detection of base modifications, such as CpG methylation, in single molecules of DNA. The most commonly used methods for long-read sequencing are nanopore developed by Oxford Nanopore Technologies (ONT) and single molecule real-time (SMRT) sequencing developed by Pacific Bioscience (PacBio). In this study, we systematically compare the performance of CpG methylation detection from long-read sequencing.
resultsWe demonstrate that CpG methylation detection from 7179 nanopore-sequenced DNA samples is highly accurate and consistent with 132 oxidative bisulfite-sequenced (oxBS) samples, isolated from the same blood draws. We introduce quality filters for CpGs that further enhance the accuracy of CpG methylation detection from nanopore-sequenced DNA, while removing at most 30% of CpGs. We evaluate the per-site performance of CpG methylation detection across different genomic features and CpG methylation rates and demonstrate how the latest R10.4 flowcell chemistry and base-calling algorithms improve methylation detection from nanopore sequencing. Additionally, we show how the methylation detection of 50 SMRT-sequenced genomes compares to nanopore sequencing and oxBS.
conclusionsThis study provides the first systematic comparison of CpG methylation detection tools for long-read sequencing methods. We compare two commonly used computational methods for the detection of CpG methylation in a large number of nanopore genomes, including samples sequenced using the latest R10.4 nanopore flowcell chemistry and 50 SMRT sequenced samples. We provide insights into the strengths and limitations of each sequencing method as well as recommendations for standardization and evaluation of tools designed for genome-scale modified base detection using long-read sequencing.
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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.