ArticleCell reports methods2022
Sensitive and reproducible cell-free methylome quantification with synthetic spike-in controls.
Article in Cell reports methods, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers, 1 of them a synthesis that pooled it.
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Who cites it
11 citing papers in PubMed, 1 synthesis or guideline pooled it, 10 citations in OpenAlex.
- Guidelines for pre-analytical conditions for assessing the methylation of circulating cell-free DNA.Clinical epigenetics · 2021Pooled it
- Circulating Cell-Free DNA Methylation Profiling Enables Detection, Distinction, and Estrogen Receptor Status Classification of Advanced Breast Cancer.Cancer research · 2026Article
- Circulating cell-free methylated DNA immunoprecipitation sequencing (cfMeDIP-seq) in oncology: from technological advances to clinical applications.NPJ precision oncology · 2026Review
- Clinical validation of a tissue-agnostic genome-wide methylome enrichment assay to monitor response to pembrolizumab.NPJ precision oncology · 2026Article
- A pan-cancer compendium of 1,294 plasma cell-free DNA methylomes and fragmentomes enabling multicancer detection.Nature cancer · 2026Article
- Early detection of multiple cancers: the era of methylation-based liquid biopsy.Frontiers in oncology · 2026Review
- Multi-Biofluid Approaches for cftDNA and cftRNA Biomarker Detection: Advances in Early Cancer Detection and Monitoring.Current issues in molecular biology · 2025Review
- Epigenetic Profiling of Cell-Free DNA in Cerebrospinal Fluid: A Novel Biomarker Approach for Metabolic Brain Diseases.Life (Basel, Switzerland) · 2025Review
- Cell-free placental DNA: What do we really know?PLoS genetics · 2024Review
- Transcriptional programming mediated by the histone demethylase KDM5C regulates dendritic cell population heterogeneity and function.Cell reports · 2024Article
- MEDIPIPE: an automated and comprehensive pipeline for cfMeDIP-seq data quality control and analysis.Bioinformatics (Oxford, England) · 2023Article
Corrections and comments
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Authors and funding
8 authors at 2 institutions in 2 countries.
Funding
Abstract
Cell-free methylated DNA immunoprecipitation sequencing (cfMeDIP-seq) identifies genomic regions with DNA methylation, using a protocol adapted to work with low-input DNA samples and with cell-free DNA (cfDNA). We developed a set of synthetic spike-in DNA controls for cfMeDIP-seq to provide a simple and inexpensive reference for quantitative normalization. We designed 54 DNA fragments with combinations of methylation status (methylated and unmethylated), fragment length (80 bp, 160 bp, 320 bp), G + C content (35%, 50%, 65%), and fraction of CpG dinucleotides within the fragment (1/80 bp, 1/40 bp, 1/20 bp). Using 0.01 ng of spike-in controls enables training a generalized linear model that absolutely quantifies methylated cfDNA in MeDIP-seq experiments. It mitigates batch effects and corrects for biases in enrichment due to known biophysical properties of DNA fragments and other technical biases.
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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.