ArticleBioinformatics (Oxford, England)2019
TPES: tumor purity estimation from SNVs.
Article in Bioinformatics (Oxford, England), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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15 citing papers in PubMed.
- Integrated genomic analyses identify oncogenic pathway interplay in hepatocarcinogenesis defining specific molecular subtypes.Nature communications · 2026Article
- Whole‑exome evolutionary profiling of osteosarcoma uncovers metastasis‑related driver mutations and generates an independently validated predictive classifier.Journal of translational medicine · 2025Article
- Patient-Derived Bladder Cancer Organoids as a Valuable Tool for Understanding Tumor Biology and Developing Personalized Treatment.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Exploration of identifying individual tumor tissue based on probabilistic model.Frontiers in oncology · 2024Article
- Variant calling enhances the identification of cancer cells in single-cell RNA sequencing data.PLoS computational biology · 2022Article
- Tumor Purity in Preclinical Mouse Tumor Models.Cancer research communications · 2022Article
- Allele-specific genomic data elucidate the role of somatic gain and copy-number neutral loss of heterozygosity in cancer.Cell systems · 2022Article
- Low Expression of AGPAT5 Is Associated With Clinical Stage and Poor Prognosis in Colorectal Cancer and Contributes to Tumour Progression.Clinical Medicine Insights. Oncology · 2022Article
- Characterization of the Genomic and Immunologic Diversity of Malignant Brain Tumors through Multisector Analysis.Cancer discovery · 2022Article
- Feasibility of a novel non-invasive swab technique for serial whole-exome sequencing of cervical tumors during chemoradiation therapy.PloS one · 2022Article
- Mutational analysis of extranodal marginal zone lymphoma using next generation sequencing.Oncology letters · 2020Article
- Purity estimation from differentially methylated sites using Illumina Infinium methylation microarray data.Cell cycle (Georgetown, Tex.) · 2020Article
- Comparative analysis of somatic variant calling on matched FF and FFPE WGS samples.BMC medical genomics · 2020Article
- GeTallele: A Method for Analysis of DNA and RNA Allele Frequency Distributions.Frontiers in bioengineering and biotechnology · 2020Article
- Comprehensive Characterization of Alternative mRNA Splicing Events in Glioblastoma: Implications for Prognosis, Molecular Subtypes, and Immune Microenvironment Remodeling.Frontiers in oncology · 2020Article
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4 authors.
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Abstract
motivationTumor purity (TP) is the proportion of cancer cells in a tumor sample. TP impacts on the accurate assessment of molecular and genomics features as assayed with NGS approaches. State-of-the-art tools mainly rely on somatic copy-number alterations (SCNA) to quantify TP and therefore fail when a tumor genome is nearly euploid, i.e. 'non-aberrant' in terms of identifiable SCNAs.
resultsWe introduce a computational method, tumor purity estimation from single-nucleotide variants (SNVs), which derives TP from the allelic fraction distribution of SNVs. On more than 7800 whole-exome sequencing data of TCGA tumor samples, it showed high concordance with a range of TP tools (Spearman's correlation between 0.68 and 0.82; >9 SNVs) and rescued TP estimates of 1, 194 samples (15%) pan-cancer. AVAILABILITY AND IMPLEMENTATION: TPES is available as an R package on CRAN and at https://bitbucket.org/l0ka/tpes.git. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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