ArticleGenome biology2017
Estimating and accounting for tumor purity in the analysis of DNA methylation data from cancer studies.
Article in Genome biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 85 papers.
What it found
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Who cites it
85 citing papers in PubMed.
- Epigenetic Markers of Cell Division and Ageing in Relation to Breast Cancer Survival.International journal of cancer · 2026Article
- Cross-Scale Convergence in Epigenetic Gene Regulation: A Perspective on Functional Enrichment Analytics for Cancer.Current issues in molecular biology · 2026Article
- DNA methylation profiling enables subclassification of mucinous ovarian carcinoma and distinguishes it from extraovarian mucinous metastases.Cell reports. Medicine · 2026Article
- DNA methylation heterogeneity in complex tumor microenvironment: Quantitative methods, influencing factors, and clinical implications.Genes & diseases · 2026Review
- Overexpression of ENDOD1 inhibits proliferation, migration, and invasion of colorectal cancer.Cell division · 2026Article
- Multiomics assessment of lung adenocarcinoma subtypes defined through tumor purity-adjusted DNA methylation.Genome medicine · 2026Article
- A review of the use of tumour DNA methylation for breast cancer subtyping and prediction of outcomes.Clinical epigenetics · 2025Review
- Ancestral Differences in Anticancer Treatment Efficacy and Their Underlying Genomic and Molecular Alterations.Cancer discovery · 2025Article
- EMixed: Probabilistic Multi-Omics Cellular Deconvolution of Bulk Omics Data.Journal of data science : JDS · 2025Article
- Tumour purity assessment with deep learning in colorectal cancer and impact on molecular analysis.The Journal of pathology · 2025Article
- Reference-free deconvolution of complex samples based on cross-cell-type differential analysis: Systematic evaluations with various feature selection options.Frontiers in genetics · 2025Article
- 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
- Tumor purity estimated from bulk DNA methylation can be used for adjusting beta values of individual samples to better reflect tumor biology.NAR genomics and bioinformatics · 2024Article
- Validating reference-based algorithms to determine cell-type heterogeneity in ovarian cancer DNA methylation studies.Scientific reports · 2024Article
- The Epigenetic Evolution of Glioma Is Determined by the IDH1 Mutation Status and Treatment Regimen.Cancer research · 2024Article
- Noninvasive Detection of Neuroendocrine Prostate Cancer through Targeted Cell-free DNA Methylation.Cancer discovery · 2024Article
- Integrative methylome and transcriptome analysis reveals epigenetic regulation ofMicrobial genomics · 2024Article
- UPP1 promotes lung adenocarcinoma progression through the induction of an immunosuppressive microenvironment.Nature communications · 2024Article
- Tumor microenvironment deconvolution identifies cell-type-independent aberrant DNA methylation and gene expression in prostate cancer.Clinical epigenetics · 2024Article
- scMD facilitates cell type deconvolution using single-cell DNA methylation references.Communications biology · 2024Article
25 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
We present a set of statistical methods for the analysis of DNA methylation microarray data, which account for tumor purity. These methods are an extension of our previously developed method for purity estimation; our updated method is flexible, efficient, and does not require data from reference samples or matched normal controls. We also present a method for incorporating purity information for differential methylation analysis. In addition, we propose a control-free differential methylation calling method when normal controls are not available. Extensive analyses of TCGA data demonstrate that our methods provide accurate results. All methods are implemented in InfiniumPurify.
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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.