ArticleNAR genomics and bioinformatics2024
Tumor purity estimated from bulk DNA methylation can be used for adjusting beta values of individual samples to better reflect tumor biology.
Article in NAR genomics and bioinformatics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Immune pathway activation in gastric cancers with LINE-1 retrotransposon overexpression and homologous recombination deficiency.Experimental & molecular medicine · 2026Article
- Genome-wide DNA methylation profiling of triple-negative breast cancer uncovers epigenetic biomarkers of tumor identity and the immune microenvironment.NPJ breast cancer · 2026Article
- Homologous recombination deficiency in primary ER-positive and HER2-negative breast cancer.Communications medicine · 2026Article
- Multiomics assessment of lung adenocarcinoma subtypes defined through tumor purity-adjusted DNA methylation.Genome medicine · 2026Article
- Molecular profiling of the Basal-like intrinsic molecular subtype in primary ER-positive HER2-negative breast cancer.Genome medicine · 2025Article
- The DNA methylation landscape of primary triple-negative breast cancer.Nature communications · 2025Article
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Authors and funding
5 authors.
Funding
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Abstract
Epigenetic deregulation through altered DNA methylation is a fundamental feature of tumorigenesis, but tumor data from bulk tissue samples contain different proportions of malignant and non-malignant cells that may confound the interpretation of DNA methylation values. The adjustment of DNA methylation data based on tumor purity has been proposed to render both genome-wide and gene-specific analyses more precise, but it requires sample purity estimates. Here we present PureBeta, a single-sample statistical framework that uses genome-wide DNA methylation data to first estimate sample purity and then adjust methylation values of individual CpGs to correct for sample impurity. Purity values estimated with the algorithm have high correlation (>0.8) to reference values obtained from DNA sequencing when applied to samples from breast carcinoma, lung adenocarcinoma, and lung squamous cell carcinoma. Methylation beta values adjusted based on purity estimates have a more binary distribution that better reflects theoretical methylation states, thus facilitating improved biological inference as shown for
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