ArticleNPJ genomic medicine2020
Association of CNVs with methylation variation.
Article in NPJ genomic medicine, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
What it found
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Who cites it
29 citing papers in PubMed, 35 citations in OpenAlex.
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- Multi-omics analysis of HLTF context-dependent regulation across TCGA cohorts revealed its potential as new biomarker in tumour.Mammalian genome : official journal of the International Mammalian Genome Society · 2026Article
- Global impact of germline structural variation on the cancer proteome.Nature communications · 2026Article
- HINN: Hierarchical Input Neural Network identifies multi-omics biomarker for cognitive decline.Research square · 2025Article
- Germline structural variations involving the pediatric brain tumor transcriptome include disease-relevant and ancestry-related genes.Acta neuropathologica communications · 2025Article
- Methylation aberrations and genomic instability synergistically drive the evolution of intrahepatic cholangiocarcinoma.Epigenomics · 2025Article
- GUIDE: a prospective cohort study for blood-based early detection of gastrointestinal cancers using targeted DNA methylation and fragmentomics sequencing.Molecular cancer · 2025Observational
- Global DNA methylation differences involving germline structural variation impact gene expression in pediatric brain tumors.Nature communications · 2025Article
- Inferring the Selective History of CNVs Using a Maximum Likelihood Model.Genome biology and evolution · 2025Article
- Benchmarking strategies for CNV calling from whole genome bisulfite data in humans.Computational and structural biotechnology journal · 2025Article
- Epigenetic reprogramming in mouse and human primordial germ cells.Experimental & molecular medicine · 2024Review
- Epigenetic diversity of genes with copy number variations among natural populations of the three-spined stickleback.Evolutionary applications · 2024Article
- BISCUIT: an efficient, standards-compliant tool suite for simultaneous genetic and epigenetic inference in bulk and single-cell studies.Nucleic acids research · 2024Article
- Epiallelic variation of non-coding RNA genes and their phenotypic consequences.Nature communications · 2024Article
- Exportin 4 DNA promoter methylation in liver fibrosis.PloS one · 2024Article
- A pan-cancer analysis revealing the role of LFNG, MFNG and RFNG in tumor prognosis and microenvironment.BMC cancer · 2023Article
- Construction of a novel prognostic model in skin cutaneous melanoma based on chemokines-related gene signature.Scientific reports · 2023Article
- Article
- 7p22.2 Microduplication: A Pathogenic CNV?Genes · 2023Article
- Rare genetic variants underlie outlying levels of DNA methylation and gene-expression.Human molecular genetics · 2023Article
Corrections and comments
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Authors and funding
10 authors at 5 institutions in 3 countries.
Funding
Abstract
Germline copy number variants (CNVs) and single-nucleotide polymorphisms (SNPs) form the basis of inter-individual genetic variation. Although the phenotypic effects of SNPs have been extensively investigated, the effects of CNVs is relatively less understood. To better characterize mechanisms by which CNVs affect cellular phenotype, we tested their association with variable CpG methylation in a genome-wide manner. Using paired CNV and methylation data from the 1000 genomes and HapMap projects, we identified genome-wide associations by methylation quantitative trait locus (mQTL) analysis. We found individual CNVs being associated with methylation of multiple CpGs and vice versa. CNV-associated methylation changes were correlated with gene expression. CNV-mQTLs were enriched for regulatory regions, transcription factor-binding sites (TFBSs), and were involved in long-range physical interactions with associated CpGs. Some CNV-mQTLs were associated with methylation of imprinted genes. Several CNV-mQTLs and/or associated genes were among those previously reported by genome-wide association studies (GWASs). We demonstrate that germline CNVs in the genome are associated with CpG methylation. Our findings suggest that structural variation together with methylation may affect cellular phenotype.
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Registered trials
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.