ArticleGenome biology2015
Whole genome bisulfite sequencing of cell-free DNA and its cellular contributors uncovers placenta hypomethylated domains.
Article in Genome biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers, 1 of them a synthesis that pooled it.
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Who cites it
45 citing papers in PubMed, 1 synthesis or guideline pooled it, 73 citations in OpenAlex.
- Guidelines for pre-analytical conditions for assessing the methylation of circulating cell-free DNA.Clinical epigenetics · 2021Pooled it
- Prenatal cell-free DNA methylome detects association with autism and maternal obesity.Communications biology · 2026Article
- Liquid biopsy epigenetics: establishing a molecular profile based on cell-free DNA.Molecular oncology · 2026Review
- Expanding the scope of non-invasive prenatal screening.Nature genetics · 2025Review
- Epigenetic profiles of tissue informative CpGs inform ALS disease status and progression.Genome medicine · 2025Article
- Circulating Cell-free DNA Fragmentomics Detection and Beyond.Aging and disease · 2025Review
- Genome-wide methylation profiling of maternal cell-free DNA using methylated DNA sequencing (MeD-seq) indicates a placental and immune-cell signature.European journal of clinical investigation · 2025Article
- Telomere length as a biomarker for fetal fraction prediction in non-invasive prenatal testing.PloS one · 2025Article
- Advancing diagnosis and early risk assessment of preeclampsia through noninvasive cell-free DNA methylation profiling.Clinical epigenetics · 2024Article
- Cell-free placental DNA: What do we really know?PLoS genetics · 2024Review
- DNA methylation and gene expression as determinants of genome-wide cell-free DNA fragmentation.Nature communications · 2024Article
- FinaleMe: Predicting DNA methylation by the fragmentation patterns of plasma cell-free DNA.Nature communications · 2024Article
- FinaleMe: Predicting DNA methylation by the fragmentation patterns of plasma cell-free DNA.bioRxiv : the preprint server for biology · 2024Article
- Accurate age prediction from blood using a small set of DNA methylation sites and a cohort-based machine learning algorithm.Cell reports methods · 2023Article
- Epigenomic signatures reveal mechanistic clues and predictive markers for autism spectrum disorder.Molecular psychiatry · 2023Review
- CRAG: de novo characterization of cell-free DNA fragmentation hotspots in plasma whole-genome sequencing.Genome medicine · 2022Article
- Cell-Free DNA Fragmentomics: A Promising Biomarker for Diagnosis, Prognosis and Prediction of Response in Breast Cancer.International journal of molecular sciences · 2022Review
- Multi-omic brain and behavioral correlates of cell-free fetal DNA methylation in macaque maternal obesity models.Nature communications · 2022Article
- Fragment size and dynamics of EGFR-mutated tumor-derived DNA provide prognostic information regarding EGFR-TKI efficacy in patients with EGFR-mutated NSCLC.Scientific reports · 2022Article
- Inferring gene expression from cell-free DNA fragmentation profiles.Nature biotechnology · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundCirculating cell-free fetal DNA has enabled non-invasive prenatal fetal aneuploidy testing without direct discrimination of the maternal and fetal DNA. Testing may be improved by specifically enriching the sample material for fetal DNA. DNA methylation may allow for such a separation of DNA; however, this depends on knowledge of the methylomes of circulating cell-free DNA and its cellular contributors.
resultsWe perform whole genome bisulfite sequencing on a set of unmatched samples including circulating cell-free DNA from non-pregnant and pregnant female donors and genomic DNA from maternal buffy coat and placenta samples. We find CpG cytosines within longer fragments are more likely to be methylated. Comparison of the methylomes of placenta and non-pregnant circulating cell-free DNA reveal many of the 51,259 identified differentially methylated regions are located in domains exhibiting consistent placenta hypomethylation across millions of consecutive bases. We find these placenta hypomethylated domains are consistently located within regions exhibiting low CpG and gene density. Differentially methylated regions identified when comparing placenta to non-pregnant circulating cell-free DNA are recapitulated in pregnant circulating cell-free DNA, confirming the ability to detect differential methylation in circulating cell-free DNA mixtures.
conclusionsWe generate methylome maps for four sample types at single-base resolution, identify a link between DNA methylation and fragment length in circulating cell-free DNA, identify differentially methylated regions between sample groups, and uncover the presence of megabase-size placenta hypomethylated domains.
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