ArticleBMC bioinformatics2015
ISOpureR: an R implementation of a computational purification algorithm of mixed tumour profiles.
Article in BMC bioinformatics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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29 citing papers in PubMed.
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- A deconvolution framework that uses single-cell sequencing plus a small benchmark data set for accurate analysis of cell type ratios in complex tissue samples.Genome research · 2025Article
- Inferring tumor purity using multi-omics data based on a uniform machine learning framework MoTP.Briefings in bioinformatics · 2024Article
- iSubGen generates integrative disease subtypes by pairwise similarity assessment.Cell reports methods · 2024Article
- Development and validation of a gene expression-based Breast Cancer Purity Score.NPJ precision oncology · 2024Article
- Computational identification and experimental verification of a novel signature based on SARS-CoV-2-related genes for predicting prognosis, immune microenvironment and therapeutic strategies in lung adenocarcinoma patients.Frontiers in immunology · 2024Article
- DeMixSC: a deconvolution framework that uses single-cell sequencing plus a small benchmark dataset for improved analysis of cell-type ratios in complex tissue samples.bioRxiv : the preprint server for biology · 2023Article
- Performance of computational algorithms to deconvolve heterogeneous bulk ovarian tumor tissue depends on experimental factors.Genome biology · 2023Article
- Histone deacetylase-mediated tumor microenvironment characteristics and synergistic immunotherapy in gastric cancer.Theranostics · 2023Article
- Tumor microenvironment: barrier or opportunity towards effective cancer therapy.Journal of biomedical science · 2022Review
- Identification of Novel Molecular Subgroups in Esophageal Adenocarcinoma to Predict Response to Neo-Adjuvant Therapies.Cancers · 2022Article
- Comparative molecular genomic analyses of a spontaneous rhesus macaque model of mismatch repair-deficient colorectal cancer.PLoS genetics · 2022Article
- Identification of Tumor Microenvironment and DNA Methylation-Related Prognostic Signature for Predicting Clinical Outcomes and Therapeutic Responses in Cervical Cancer.Frontiers in molecular biosciences · 2022Article
- CPDR: An R Package of Recommending Personalized Drugs for Cancer Patients by Reversing the Individual's Disease-Related Signature.Frontiers in pharmacology · 2022Article
- The effect of tissue composition on gene co-expression.Briefings in bioinformatics · 2021Review
- A reference profile-free deconvolution method to infer cancer cell-intrinsic subtypes and tumor-type-specific stromal profiles.Genome medicine · 2020Article
- Optimization and expansion of non-negative matrix factorization.BMC bioinformatics · 2020Article
- Comprehensive Characterization of Alternative mRNA Splicing Events in Glioblastoma: Implications for Prognosis, Molecular Subtypes, and Immune Microenvironment Remodeling.Frontiers in oncology · 2020Article
- Systematic Assessment of Tumor Purity and Its Clinical Implications.JCO precision oncology · 2020Article
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7 authors.
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Abstract
backgroundTumour samples containing distinct sub-populations of cancer and normal cells present challenges in the development of reproducible biomarkers, as these biomarkers are based on bulk signals from mixed tumour profiles. ISOpure is the only mRNA computational purification method to date that does not require a paired tumour-normal sample, provides a personalized cancer profile for each patient, and has been tested on clinical data. Replacing mixed tumour profiles with ISOpure-preprocessed cancer profiles led to better prognostic gene signatures for lung and prostate cancer.
resultsTo simplify the integration of ISOpure into standard R-based bioinformatics analysis pipelines, the algorithm has been implemented as an R package. The ISOpureR package performs analogously to the original code in estimating the fraction of cancer cells and the patient cancer mRNA abundance profile from tumour samples in four cancer datasets.
conclusionsThe ISOpureR package estimates the fraction of cancer cells and personalized patient cancer mRNA abundance profile from a mixed tumour profile. This open-source R implementation enables integration into existing computational pipelines, as well as easy testing, modification and extension of the model.
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