ArticleJCO precision oncology2020
Systematic Assessment of Tumor Purity and Its Clinical Implications.
Article in JCO precision oncology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed, 62 citations in OpenAlex.
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- GBMPurity: A machine learning tool for estimating glioblastoma tumor purity from bulk RNA-sequencing data.Neuro-oncology · 2025Article
- Utility of a Novel High-Sensitivity Multiplex Companion Diagnostic Test Using Formalin-Fixed Paraffin-Embedded Cell Block Materials of Non-small Cell Lung Cancer.Cancer medicine · 2025Article
- Simulation-guided pan-cancer analysis identifies a novel regulator of CpG island hypermethylation heterogeneity.Briefings in bioinformatics · 2025Article
- Proteogenomic discovery ofScience advances · 2025Article
- Tumour purity assessment with deep learning in colorectal cancer and impact on molecular analysis.The Journal of pathology · 2025Article
- Crosstalk Between Immunity and Oncogenes Within the Tumor Microenvironment of HPV-Associated Cervical Squamous Cell Carcinoma.OncoTargets and therapy · 2025Article
- VarNMF: non-negative probabilistic factorization with source variation.Bioinformatics (Oxford, England) · 2024Article
- Inferring tumor purity using multi-omics data based on a uniform machine learning framework MoTP.Briefings in bioinformatics · 2024Article
- Development and validation of a gene expression-based Breast Cancer Purity Score.NPJ precision oncology · 2024Article
- Evaluation of the Use of Cell Lines in Studies of Selenium-Dependent Glutathione Peroxidase 2 (GPX2) Involvement in Colorectal Cancer.Diseases (Basel, Switzerland) · 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
- Artificial intelligence algorithm for neoplastic cell percentage estimation and its application to copy number variation in urinary tract cancer.Journal of pathology and translational medicine · 2024Article
Corrections and comments
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Authors and funding
15 authors at 10 institutions in 4 countries.
Funding
Abstract
purposeThe tumor microenvironment is complex, comprising heterogeneous cellular populations. As molecular profiles are frequently generated using bulk tissue sections, they represent an admixture of multiple cell types (including immune, stromal, and cancer cells) interacting with each other. Therefore, these molecular profiles are confounded by signals emanating from many cell types. Accurate assessment of residual cancer cell fraction is crucial for parameterization and interpretation of genomic analyses, as well as for accurately interpreting the clinical properties of the tumor. MATERIALS AND
methodsTo benchmark cancer cell fraction estimation methods, 10 estimators were applied to a clinical cohort of 333 patients with prostate cancer. These methods include gold-standard multiobserver pathology estimates, as well as estimates inferred from genome, epigenome, and transcriptome data. In addition, two methods based on genomic and transcriptomic profiles were used to quantify tumor purity in 4,497 tumors across 12 cancer types. Bulk mRNA and microRNA profiles were subject to in silico deconvolution to estimate cancer cell-specific mRNA and microRNA profiles.
resultsWe present a systematic comparison of 10 tumor purity estimation methods on a cohort of 333 prostate tumors. We quantify variation among purity estimation methods and demonstrate how this influences interpretation of clinico-genomic analyses. Our data show poor concordance between pathologic and molecular purity estimates, necessitating caution when interpreting molecular results. Limited concordance between DNA- and mRNA-derived purity estimates remained a general pan-cancer phenomenon when tested in an additional 4,497 tumors spanning 12 cancer types.
conclusionThe choice of tumor purity estimation method may have a profound impact on the interpretation of genomic assays. Taken together, these data highlight the need for improved assessment of tumor purity and quantitation of its influences on the molecular hallmarks of cancers.
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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.