ArticleNature communications2020
Detection of haplotype-dependent allele-specific DNA methylation in WGBS data.
Article in Nature communications, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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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.
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Who cites it
18 citing papers in PubMed.
- asms: finding allele-specific methylation in human genomes without phasing.NAR genomics and bioinformatics · 2026Article
- DNA Methylation Stochasticity Is Linked to Transcriptional Variability and Convergent Epigenetic Disruption across Genetic Subtypes of Acute Myeloid Leukemia.Cancer research · 2026Article
- nanoASM: Long-Read Allele-Specific DNA Methylation Profiling Enables Functional Annotation of Regulatory Noncoding Variants in Human Prostate Tissues.bioRxiv : the preprint server for biology · 2026Article
- Computational analysis of DNA methylation from long-read sequencing.Nature reviews. Genetics · 2025Review
- Genetic/epigenetic DNA markers for linking suspects and tissues in complex crime scenes.Briefings in bioinformatics · 2025Article
- Expanding Upon Genomics in Rare Diseases: Epigenomic Insights.International journal of molecular sciences · 2024Review
- bsgenova: an accurate, robust, and fast genotype caller for bisulfite-sequencing data.BMC bioinformatics · 2024Article
- Epigenomic insights into common human disease pathology.Cellular and molecular life sciences : CMLS · 2024Review
- Reply to: Genetic differentiation at probe SNPs leads to spurious results in meQTL discovery.Communications biology · 2023Article
- Identification of intergenerational epigenetic inheritance by whole genome DNA methylation analysis in trios.Scientific reports · 2023Article
- Genome-wide single-molecule analysis of long-read DNA methylation reveals heterogeneous patterns at heterochromatin that reflect nucleosome organisation.PLoS genetics · 2023Article
- DNA methylation entropy is associated with DNA sequence features and developmental epigenetic divergence.Nucleic acids research · 2023Article
- cvlr: finding heterogeneously methylated genomic regions using ONT reads.Bioinformatics advances · 2023Article
- MC profiling: a novel approach to analyze DNA methylation heterogeneity in genome-wide bisulfite sequencing data.NAR genomics and bioinformatics · 2022Article
- ASMdb: a comprehensive database for allele-specific DNA methylation in diverse organisms.Nucleic acids research · 2022Article
- A novel workflow for the qualitative analysis of DNA methylation data.Computational and structural biotechnology journal · 2022Article
- Estimating DNA methylation potential energy landscapes from nanopore sequencing data.Scientific reports · 2021Article
- Investigating Different DNA Methylation Patterns at the Resolution of Methylation Haplotypes.Frontiers in genetics · 2021Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
In heterozygous genomes, allele-specific measurements can reveal biologically significant differences in DNA methylation between homologous alleles associated with local changes in genetic sequence. Current approaches for detecting such events from whole-genome bisulfite sequencing (WGBS) data perform statistically independent marginal analysis at individual cytosine-phosphate-guanine (CpG) sites, thus ignoring correlations in the methylation state, or carry-out a joint statistical analysis of methylation patterns at four CpG sites producing unreliable statistical evidence. Here, we employ the one-dimensional Ising model of statistical physics and develop a method for detecting allele-specific methylation (ASM) events within segments of DNA containing clusters of linked single-nucleotide polymorphisms (SNPs), called haplotypes. Comparisons with existing approaches using simulated and real WGBS data show that our method provides an improved fit to data, especially when considering large haplotypes. Importantly, the method employs robust hypothesis testing for detecting statistically significant imbalances in mean methylation level and methylation entropy, as well as for identifying haplotypes for which the genetic variant carries significant information about the methylation state. As such, our ASM analysis approach can potentially lead to biological discoveries with important implications for the genetics of complex human diseases.
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