ArticleGenome biology2020
Allele-specific DNA methylation is increased in cancers and its dense mapping in normal plus neoplastic cells increases the yield of disease-associated regulatory SNPs.
Article in Genome biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed, 44 citations in OpenAlex.
- asms: finding allele-specific methylation in human genomes without phasing.NAR genomics and bioinformatics · 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
- Landscape of Allele-Specific Expression in Prostate Cancer Reveals Recurrent, Stage-Specific Events in AR Signaling and Resistance Pathways.Molecular cancer research : MCR · 2026Article
- Comprehensive detection of genetic and epigenetic alterations in cancer using long reads with TumorLens.medRxiv : the preprint server for health sciences · 2026Article
- CMC-WDTK: CpG methylation change prediction by a weight-sharing dual-branch Transformer-Kolmogorov-Arnold network model.BMC genomics · 2026Article
- Epigenetic networks coordinate DNA methylation across the genome.Molecular therapy : the journal of the American Society of Gene Therapy · 2025Review
- CanASM: a comprehensive database for genome-wide allele-specific DNA methylation identification and annotation in cancer.BMC genomics · 2025Article
- MethylBERT enables read-level DNA methylation pattern identification and tumour deconvolution using a Transformer-based model.Nature communications · 2025Article
- Potential impact of omentin-1 genetic variants on perineural invasion in prostate cancer.Journal of Cancer · 2025Article
- Expanding Upon Genomics in Rare Diseases: Epigenomic Insights.International journal of molecular sciences · 2024Review
- Hypomethylation at H19DMR in penile squamous cell carcinoma is not related to HPV infection.Epigenetics · 2024Article
- ChIP-Atlas 3.0: a data-mining suite to explore chromosome architecture together with large-scale regulome data.Nucleic acids research · 2024Article
- Rockfish: A transformer-based model for accurate 5-methylcytosine prediction from nanopore sequencing.Nature communications · 2024Article
- Neural-net-based cell deconvolution from DNA methylation reveals tumor microenvironment associated with cancer prognosis.NAR cancer · 2024Article
- Genome-wide screening and functional validation of methylation barriers near promoters.Nucleic acids research · 2024Article
- Investigating the potential of single-cell DNA methylation data to detect allele-specific methylation and imprinting.American journal of human genetics · 2024Article
- Genetic variation in the human leukocyte antigen region confers susceptibility to Clostridioides difficile infection.Scientific reports · 2023Article
- Methylomics and cancer: the current state of methylation profiling and marker development for clinical care.Cancer cell international · 2023Review
- Long-read sequencing of diagnosis and post-therapy medulloblastoma reveals complex rearrangement patterns and epigenetic signatures.Cell genomics · 2023Article
- Defining clonal hematopoiesis of indeterminate potential: evolutionary dynamics and detection under aging and inflammation.Cold Spring Harbor molecular case studies · 2023Review
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Authors and funding
26 authors at 6 institutions in 2 countries.
Funding
Abstract
backgroundMapping of allele-specific DNA methylation (ASM) can be a post-GWAS strategy for localizing regulatory sequence polymorphisms (rSNPs). The advantages of this approach, and the mechanisms underlying ASM in normal and neoplastic cells, remain to be clarified.
resultsWe perform whole genome methyl-seq on diverse normal cells and tissues and three cancer types. After excluding imprinting, the data pinpoint 15,112 high-confidence ASM differentially methylated regions, of which 1838 contain SNPs in strong linkage disequilibrium or coinciding with GWAS peaks. ASM frequencies are increased in cancers versus matched normal tissues, due to widespread allele-specific hypomethylation and focal allele-specific hypermethylation in poised chromatin. Cancer cells show increased allele switching at ASM loci, but disruptive SNPs in specific classes of CTCF and transcription factor binding motifs are similarly correlated with ASM in cancer and non-cancer. Rare somatic mutations affecting these same motif classes track with de novo ASM. Allele-specific transcription factor binding from ChIP-seq is enriched among ASM loci, but most ASM differentially methylated regions lack such annotations, and some are found in otherwise uninformative "chromatin deserts."
conclusionsASM is increased in cancers but occurs by a shared mechanism involving disruptive SNPs in CTCF and transcription factor binding sites in both normal and neoplastic cells. Dense ASM mapping in normal plus cancer samples reveals candidate rSNPs that are difficult to find by other approaches. Together with GWAS data, these rSNPs can nominate specific transcriptional pathways in susceptibility to autoimmune, cardiometabolic, neuropsychiatric, and neoplastic diseases.
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