ArticleGenome biology2024
CelFiE-ISH: a probabilistic model for multi-cell type deconvolution from single-molecule DNA methylation haplotypes.
Article in Genome biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Cell-to-cell variability and gain of methylation at polycomb CpG islands as a hallmark of aging.Nature communications · 2026Article
- From Spatial Epigenomes to Clinical Diagnostics: Integrative Methylomics Across Scales and Modalities.International journal of molecular sciences · 2026Review
- Long-read sequencing identifies aberrant fragmentation patterns linked to elevated cell-free DNA levels in cancer.Genome biology · 2026Article
- Article
- Haplotype-resolved DNA methylation at theNPJ dementia · 2026Article
- Application of a modified MSRE-qPCR method for detecting circulating cell-free DNA methylation in cervical cancer.Frontiers in oncology · 2026Article
- Evolution of genome-wide methylation profiling technologies.Genome research · 2025Review
- cfTools: an R/Bioconductor package for deconvolving cell-free DNA via methylation analysis.Bioinformatics advances · 2025Article
- Author Correction: CelFiE-ISH: a probabilistic model for multi-cell type deconvolution from single-molecule DNA methylation haplotypes.Genome biology · 2024Article
- CelFiE-ISH: a probabilistic model for multi-cell type deconvolution from single-molecule DNA methylation haplotypes.Genome biology · 2024Article
- Tissue informative cell-free DNA methylation sites in amyotrophic lateral sclerosis.medRxiv : the preprint server for health sciences · 2024Article
Corrections and comments
- Erratum issued
Authors and funding
6 authors.
Funding
Abstract
Deconvolution methods infer quantitative cell type estimates from bulk measurement of mixed samples including blood and tissue. DNA methylation sequencing measures multiple CpGs per read, but few existing deconvolution methods leverage this within-read information. We develop CelFiE-ISH, which extends an existing method (CelFiE) to use within-read haplotype information. CelFiE-ISH outperforms CelFiE and other existing methods, achieving 30% better accuracy and more sensitive detection of rare cell types. We also demonstrate the importance of marker selection and of tailoring markers for haplotype-aware methods. While here we use gold-standard short-read sequencing data, haplotype-aware methods will be well-suited for long-read sequencing.
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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.