ArticleGenome research2015
A pooling-based approach to mapping genetic variants associated with DNA methylation.
Article in Genome research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
What it found
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The trial behind it
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
19 citing papers in PubMed, 39 citations in OpenAlex.
- MammaTrace - a tumor naïve cell-free DNA methylation test for minimal residual disease in breast cancer.NPJ precision oncology · 2026Article
- Chromatin activity identifies differential gene regulation across human ancestries.Genome biology · 2024Article
- Evaluating the challenges and reproducibility of studies investigating DNA methylation signatures of psychological stress.Epigenomics · 2022Review
- DNA Methylation in Ovarian Cancer Susceptibility.Cancers · 2020Review
- Molecular mechanisms of coronary disease revealed using quantitative trait loci for TCF21 binding, chromatin accessibility, and chromosomal looping.Genome biology · 2020Article
- IMAGE: high-powered detection of genetic effects on DNA methylation using integrated methylation QTL mapping and allele-specific analysis.Genome biology · 2019Article
- Fine-mappingeLife · 2019Article
- Whole-genome bisulfite sequencing with improved accuracy and cost.Genome research · 2018Article
- The Post-GWAS Era: From Association to Function.American journal of human genetics · 2018Review
- Exploring DNA variant segregation types in pooled genome sequencing enables effective mapping of weeping trait in Malus.Journal of experimental botany · 2018Article
- Methylation of the genes ROD1, NLRC5, and HKR1 is associated with aging in Hainan centenarians.BMC medical genomics · 2018Article
- Regions of common inter-individual DNA methylation differences in human monocytes: genetic basis and potential function.Epigenetics & chromatin · 2017Article
- Predicting the impact of non-coding variants on DNA methylation.Nucleic acids research · 2017Article
- DeepCpG: accurate prediction of single-cell DNA methylation states using deep learning.Genome biology · 2017Article
- Fishing for Function in the Human Gene Pool.Trends in genetics : TIG · 2016Article
- Article
- Systematic identification of genetic influences on methylation across the human life course.Genome biology · 2016Article
- Whole-genome bisulfite sequencing of cell-free DNA identifies signature associated with metastatic breast cancer.Clinical epigenetics · 2015Article
- Methyl-SNP-seq reveals dual readouts of methylome and variome at molecule resolution while enabling target enrichment.Genome researchArticle
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
Abstract
DNA methylation is an epigenetic modification that plays a key role in gene regulation. Previous studies have investigated its genetic basis by mapping genetic variants that are associated with DNA methylation at specific sites, but these have been limited to microarrays that cover <2% of the genome and cannot account for allele-specific methylation (ASM). Other studies have performed whole-genome bisulfite sequencing on a few individuals, but these lack statistical power to identify variants associated with DNA methylation. We present a novel approach in which bisulfite-treated DNA from many individuals is sequenced together in a single pool, resulting in a truly genome-wide map of DNA methylation. Compared to methods that do not account for ASM, our approach increases statistical power to detect associations while sharply reducing cost, effort, and experimental variability. As a proof of concept, we generated deep sequencing data from a pool of 60 human cell lines; we evaluated almost twice as many CpGs as the largest microarray studies and identified more than 2000 genetic variants associated with DNA methylation. We found that these variants are highly enriched for associations with chromatin accessibility and CTCF binding but are less likely to be associated with traits indirectly linked to DNA, such as gene expression and disease phenotypes. In summary, our approach allows genome-wide mapping of genetic variants associated with DNA methylation in any tissue of any species, without the need for individual-level genotype or methylation data.
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What OpenQuestion holds
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.