ArticleCommunications biology2020
MethylResolver-a method for deconvoluting bulk DNA methylation profiles into known and unknown cell contents.
Article in Communications biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
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Who cites it
49 citing papers in PubMed, 89 citations in OpenAlex.
- Decomposition-driven biomarker identification enhances non-invasive early cancer detection.iScience · 2026Article
- DeOPUS: cellular deconvolution via optimized power-transformed unmixing with shrinkage.Briefings in bioinformatics · 2026Article
- DNA methylation-based immune cell profiling in mouse blood using MouseRS-CMD.Genome biology · 2026Article
- Construction and validation of a novel prognostic risk model in cervical cancer: integrating lactylation-related genes linked to radiotherapy‑associated transcriptional changes.Discover oncology · 2026Article
- From Spatial Epigenomes to Clinical Diagnostics: Integrative Methylomics Across Scales and Modalities.International journal of molecular sciences · 2026Review
- Meningioma microenvironment harbors a rich immune landscape that evolves with biological state.Neuro-oncology · 2026Article
- Identification and validation of liquid biopsy-based methylation biomarkers for germ cell tumor subtypes.Communications medicine · 2026Article
- Molecular immune signature identifies microglia and NK cell infiltration as a favorable prognostic marker in adult-type high-grade glioma.ESMO open · 2026Article
- Immune Cell Type-Specific DNA Methylation Regions Associate With 24-Hour Blood Pressure Regulation in Black People.Journal of the American Heart Association · 2026Article
- Guidelines on optimizing DNA methylation reference panels for cell-type deconvolution.Communications biology · 2026Article
- Multiomics assessment of lung adenocarcinoma subtypes defined through tumor purity-adjusted DNA methylation.Genome medicine · 2026Article
- Article
- Use of DNA Methylation Profiling as a Molecular Classification Tool for Paediatric Central Nervous System Tumours: A Middle-Income Country Population-Based Study.Neuropathology and applied neurobiology · 2025Article
- Computational analysis of DNA methylation from long-read sequencing.Nature reviews. Genetics · 2025Review
- Simulation-guided pan-cancer analysis identifies a novel regulator of CpG island hypermethylation heterogeneity.Briefings in bioinformatics · 2025Article
- Examining cellular heterogeneity in human DNA methylation studies: Overview and recommendations.STAR protocols · 2025Review
- Spatial deconvolution from bulk DNA methylation profiles determines intratumoral epigenetic heterogeneity.Cell & bioscience · 2025Article
- Unifying DNA methylation-basedBioinformatics advances · 2025Article
- Multimodal genome-wide survey of progressing and non-progressing breast ductal carcinoma in-situ.Breast cancer research : BCR · 2024Article
- Glioma immune microenvironment composition calculator (GIMiCC): a method of estimating the proportions of eighteen cell types from DNA methylation microarray data.Acta neuropathologica communications · 2024Article
Corrections and comments
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Authors and funding
3 authors at 3 institutions in 2 countries.
Funding
Abstract
Bulk tissue DNA methylation profiling has been used to examine epigenetic mechanisms and biomarkers of complex diseases such as cancer. However, heterogeneity of cellular content in tissues complicates result interpretation and utility. In silico deconvolution of cellular fractions from bulk tissue data offers a fast and inexpensive alternative to experimentally measuring such fractions. In this study, we report the design, implementation, and benchmarking of MethylResolver, a Least Trimmed Squares regression-based method for inferring leukocyte subset fractions from methylation profiles of tumor admixtures. Compared to previous approaches MethylResolver is more accurate as unknown cellular content in the mixture increases and is able to resolve tumor purity-scaled immune cell-type fractions without a cancer-specific signature. We also present a pan-cancer deconvolution of TCGA, recapitulating that high eosinophil fraction predicts improved cervical carcinoma survival and identifying elevated B cell fraction as a previously unreported predictor of poor survival for papillary renal cell carcinoma.
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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.