ArticleComputational and structural biotechnology journal2020
PreMSIm: An R package for predicting microsatellite instability from the expression profiling of a gene panel in cancer.
Article in Computational and structural biotechnology journal, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers, 1 of them a synthesis that pooled it.
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46 citing papers in PubMed, 1 synthesis or guideline pooled it, 114 citations in OpenAlex.
- Tumor microenvironment-aware, single-transcriptome prediction of microsatellite instability in colorectal cancer using meta-analysis.Scientific reports · 2022Pooled it
- EMMA-STRAT: a multi-omics based machine learning framework for stratification of endometrial carcinoma molecular subtypes and MSI status.BioData mining · 2026Article
- The Aberrant Activation of NLRP3 in Microsatellites Stability Colon Cancer Promotes M2 Macrophage Polarization Based on the TCGA Database and Tissue Microarray Analysis.Cancer reports (Hoboken, N.J.) · 2026Article
- PRMT5 Inhibitor Synergizes with Chemotherapy to Induce Resembling Mismatch Repair Deficiency and Enhance Anti-TIGIT Therapy in Microsatellite-Stable Colorectal Cancer.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Molecular and functional profiling unravels targetable vulnerabilities in colorectal cancer.Molecular oncology · 2025Article
- Identification of USP39 as a prognostic and predictive biomarker for determining the response to immunotherapy in pancreatic cancer.BMC cancer · 2025Article
- Article
- Integration of Graph Neural Networks and multi-omics analysis identify the predictive factor and key gene for immunotherapy response and prognosis of bladder cancer.Journal of translational medicine · 2024Article
- DNA damage response in breast cancer and its significant role in guiding novel precise therapies.Biomarker research · 2024Review
- MSIsensor-RNA: Microsatellite Instability Detection for Bulk and Single-cell Gene Expression Data.Genomics, proteomics & bioinformatics · 2024Article
- Detecting microsatellite instability by length comparison of microsatellites in the 3' untranslated region with RNA-seq.Briefings in bioinformatics · 2024Article
- Performance assessment of computational tools to detect microsatellite instability.Briefings in bioinformatics · 2024Article
- Accelerated Aging and Microsatellite Instability in Recessive Dystrophic Epidermolysis Bullosa-Associated Cutaneous Squamous Cell Carcinoma.The Journal of investigative dermatology · 2024Article
- Multi-omics Analysis Identifies Hypoxia Subtypes and S100A2 as an Immunosuppressive Factor in Cervical Cancer.Reproductive sciences (Thousand Oaks, Calif.) · 2024Article
- Long-read sequencing reveals the landscape of aberrant alternative splicing and novel therapeutic target in colorectal cancer.Genome medicine · 2023Article
- Novel prognostic gene signature for pancreatic ductal adenocarcinoma based on hypoxia.World journal of surgical oncology · 2023Article
- Cuproptosis-related risk score based on machine learning algorithm predicts prognosis and characterizes tumor microenvironment in head and neck squamous carcinomas.Scientific reports · 2023Article
- Integrated clinical genomic analysis reveals xenobiotic metabolic genes are downregulated in meningiomas of current smokers.Journal of neuro-oncology · 2023Article
- BRD4 inhibition impairs DNA mismatch repair, induces mismatch repair mutation signatures and creates therapeutic vulnerability to immune checkpoint blockade in MMR-proficient tumors.Journal for immunotherapy of cancer · 2023Article
- APC mutation correlated with poor response of immunotherapy in colon cancer.BMC gastroenterology · 2023Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Microsatellite instability (MSI) is a genomic property of the cancers with defective DNA mismatch repair and is a useful marker for cancer diagnosis and treatment in diverse cancer types. In particular, MSI has been associated with the active immune checkpoint blockade therapy response in cancer. Most of computational methods for predicting MSI are based on DNA sequencing data and a few are based on mRNA expression data. Using the RNA-Seq pan-cancer datasets for three cancer cohorts (colon, gastric, and endometrial cancers) from The Cancer Genome Atlas (TCGA) program, we developed an algorithm (PreMSIm) for predicting MSI from the expression profiling of a 15-gene panel in cancer. We demonstrated that PreMSIm had high prediction performance in predicting MSI in most cases using both RNA-Seq and microarray gene expression datasets. Moreover, PreMSIm displayed superior or comparable performance versus other DNA or mRNA-based methods. We conclude that PreMSIm has the potential to provide an alternative approach for identifying MSI in cancer.
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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.