ArticleNucleic acids research2020
Quantitative comparison of within-sample heterogeneity scores for DNA methylation data.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed.
- Article
- Epigenetic Mechanisms in Sepsis-Induced Cardiomyopathy: From Pathophysiology to Therapeutic Targets.International journal of molecular sciences · 2026Review
- DNA methylation heterogeneity in complex tumor microenvironment: Quantitative methods, influencing factors, and clinical implications.Genes & diseases · 2026Review
- MPCI: A novel metric for quantifying DNA methylation patterns in NGS data.PLoS computational biology · 2026Article
- OpTiles: an R package for adaptive tiling and methylation variability profiling.Bioinformatics (Oxford, England) · 2025Article
- Epigenetic drift score captures directional methylation variability and links aging to transcriptional, metabolic, and genetic alterations.Genome research · 2025Article
- Aging by the clock and yet without a program.Nature aging · 2025Review
- Epigenetic networks coordinate DNA methylation across the genome.Molecular therapy : the journal of the American Society of Gene Therapy · 2025Review
- Computational analysis of DNA methylation from long-read sequencing.Nature reviews. Genetics · 2025Review
- DNA methylation cooperates with genomic alterations during non-small cell lung cancer evolution.Nature genetics · 2025Article
- Article
- A Novel Framework for the Design of Minimized Epigenetic Clocks Using the Analysis of DNA Methylation Heterogeneity.International journal of molecular sciences · 2025Article
- Article
- Increased local DNA methylation disorder in AMLs with DNMT3A-destabilizing variants and its clinical implication.Nature communications · 2025Article
- DNA methylation in mammalian development and disease.Nature reviews. Genetics · 2025Review
- EpiCHAOS: a metric to quantify epigenomic heterogeneity in single-cell data.Genome biology · 2024Article
- DNA methylation heterogeneity attributable to a complex tumor immune microenvironment prompts prognostic risk in glioma.Epigenetics · 2024Article
- Charting epimutation dynamics in human hematopoietic differentiation.Blood science (Baltimore, Md.) · 2024Article
- Age Prediction Using DNA Methylation Heterogeneity Metrics.International journal of molecular sciences · 2024Article
- Article
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA methylation is an epigenetic mark with important regulatory roles in cellular identity and can be quantified at base resolution using bisulfite sequencing. Most studies are limited to the average DNA methylation levels of individual CpGs and thus neglect heterogeneity within the profiled cell populations. To assess this within-sample heterogeneity (WSH) several window-based scores that quantify variability in DNA methylation in sequencing reads have been proposed. We performed the first systematic comparison of four published WSH scores based on simulated and publicly available datasets. Moreover, we propose two new scores and provide guidelines for selecting appropriate scores to address cell-type heterogeneity, cellular contamination and allele-specific methylation. Most of the measures were sensitive in detecting DNA methylation heterogeneity in these scenarios, while we detected differences in susceptibility to technical bias. Using recently published DNA methylation profiles of Ewing sarcoma samples, we show that DNA methylation heterogeneity provides information complementary to the DNA methylation level. WSH scores are powerful tools for estimating variance in DNA methylation patterns and have the potential for detecting novel disease-associated genomic loci not captured by established statistics. We provide an R-package implementing the WSH scores for integration into analysis workflows.
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