ArticleEpigenetics & chromatin2021
Evaluation of whole-genome DNA methylation sequencing library preparation protocols.
Article in Epigenetics & chromatin, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed, 91 citations in OpenAlex.
- Detection of differential DNA methylation in date palm (Phoenix dactylifera L.) vitroplants using whole genome bisulfite sequencing analysis.BMC plant biology · 2026Article
- Development, characterization, and inter-laboratory validation of methylated human cell free DNA candidate reference materials.Clinical epigenetics · 2026Article
- Cardiac epigenome in heart development and disease.Nature reviews. Cardiology · 2026Review
- Laser Capture Microdissection Followed by DNA Methylation Profiling.Methods in molecular biology (Clifton, N.J.) · 2026Article
- 5mC and 5hmC methylation sequencing: the power of 6-base sequencing in a multiomic era.Epigenomics · 2026Review
- An optimized protocol to detect high-throughput DNA methylation from custom targeted sequences on 96 samples simultaneously.FEBS open bio · 2025Article
- Pipeline Olympics: continuable benchmarking of computational workflows for DNA methylation sequencing data against an experimental gold standard.Nucleic acids research · 2025Article
- Comprehensive comparison of enzymatic and bisulfite DNA methylation analysis in clinically relevant samples.Clinical epigenetics · 2025Article
- Comparison of current methods for genome-wide DNA methylation profiling.Epigenetics & chromatin · 2025Article
- Comparison of enzymatic and bisulfite conversion of circulating cell-free tumor DNA for DNA methylation analyses.Clinical epigenetics · 2025Article
- Biases from Oxford Nanopore library preparation kits and their effects on microbiome and genome analysis.BMC genomics · 2025Article
- Comparison of enzymatic and bisulfite-based methods for sequencing-based cell-free DNA methylation profiling.Frontiers in epigenetics and epigenomics · 2025Article
- Improved detection of methylation in ancient DNA.Genome biology · 2024Article
- MetDecode: methylation-based deconvolution of cell-free DNA for noninvasive multi-cancer typing.Bioinformatics (Oxford, England) · 2024Article
- DNA methylation of exercise-responsive genes differs between trained and untrained men.BMC biology · 2024Article
- BISCUIT: an efficient, standards-compliant tool suite for simultaneous genetic and epigenetic inference in bulk and single-cell studies.Nucleic acids research · 2024Article
- Use of Enzymatically Converted Cell-Free DNA (cfDNA) Data for Copy Number Variation-Linked Fragmentation Analysis Allows for Early Colorectal Cancer Detection.International journal of molecular sciences · 2024Article
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- Genomic and epigenomic integrative subtypes of renal cell carcinoma in a Japanese cohort.Nature communications · 2023Article
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Authors and funding
11 authors at 3 institutions in 1 country.
Funding
Abstract
backgroundWith rapidly dropping sequencing cost, the popularity of whole-genome DNA methylation sequencing has been on the rise. Multiple library preparation protocols currently exist. We have performed 22 whole-genome DNA methylation sequencing experiments on snap frozen human samples, and extensively benchmarked common library preparation protocols for whole-genome DNA methylation sequencing, including three traditional bisulfite-based protocols and a new enzyme-based protocol. In addition, different input DNA quantities were compared for two kits compatible with a reduced starting quantity. In addition, we also present bioinformatic analysis pipelines for sequencing data from each of these library types.
resultsAn assortment of metrics were collected for each kit, including raw read statistics, library quality and uniformity metrics, cytosine retention, and CpG beta value consistency between technical replicates. Overall, the NEBNext Enzymatic Methyl-seq and Swift Accel-NGS Methyl-Seq kits performed quantitatively better than the other two protocols. In addition, the NEB and Swift kits performed well at low-input amounts, validating their utility in applications where DNA is the limiting factor.
resultsThe NEBNext Enzymatic Methyl-seq kit appeared to be the best option for whole-genome DNA methylation sequencing of high-quality DNA, closely followed by the Swift kit, which potentially works better for degraded samples. Further, a general bioinformatic pipeline is applicable across the four protocols, with the exception of extra trimming needed for the Swift Biosciences's Accel-NGS Methyl-Seq protocol to remove the Adaptase sequence.
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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.