ArticleBriefings in bioinformatics2021
MSIsensor-ct: microsatellite instability detection using cfDNA sequencing data.
Article in Briefings in bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Analysis of microsatellite instability intensity in single-cell resolution with scMnT reveals tumor heterogeneity in colorectal cancer.Briefings in bioinformatics · 2026Article
- T Cell Exhaustion and Dendritic Cell-Mediated Tertiary Lymphoid Structures (TLSs) Modulation Affect Response to Neoadjuvant Chemoradiotherapy in Microsatellite Stable Rectal Cancer.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Advances in Hereditary Colorectal Cancer: How Precision Medicine Is Changing the Game.Cancers · 2025Review
- Unraveling the role of PREX2 mutations as a biomarker for immunotherapy response in colorectal cancer.Cancer biomarkers : section A of Disease markers · 2025Article
- Validation of a liquid biopsy assay with increased sensitivity for clinical comprehensive genomic profiling.The journal of liquid biopsy · 2025Article
- Decoding the molecular landscape: HER2 and PD-L1 in advanced gastric cancer.Frontiers in immunology · 2025Article
- scMSI: Accurately inferring the sub-clonal Micro-Satellite status by an integrated deconvolution model on length spectrum.PLoS computational biology · 2024Article
- Targeted panel sequencing of pharmacogenes and oncodrivers in colorectal cancer patients reveals genes with prognostic significance.Human genomics · 2024Article
- Unraveling EGFR-TKI resistance in lung cancer with high PD-L1 or TMB in EGFR-sensitive mutations.Respiratory research · 2024Article
- Clinical implications of PD-L1 expression and pathway-related molecular subtypes in advanced Asian colorectal cancer patients.American journal of cancer research · 2024Article
- Prognostic potential of whole exome sequencing in the clinical management of metachronous colorectal cancer liver metastases.Cancer cell international · 2023Article
- Comprehensive genomic characterization of sporadic synchronous colorectal cancer: Implications for treatment optimization and clinical outcome.Cell reports. Medicine · 2023Article
- Specific Mutations in APC, with Prognostic Implications in Metastatic Colorectal Cancer.Cancer research and treatment · 2023Article
- Microsatellite instability assessment is instrumental for Predictive, Preventive and Personalised Medicine: status quo and outlook.The EPMA journal · 2023Review
- Relative Risk of Bladder and Kidney Cancer in Lynch Syndrome: Systematic Review and Meta-Analysis.Cancers · 2023Review
- Circulating Tumor DNA-A Novel Biomarker of Tumor Progression and Its Favorable Detection Techniques.Cancers · 2022Review
- Liquid Biopsy as a Source of Nucleic Acid Biomarkers in the Diagnosis and Management of Lynch Syndrome.International journal of molecular sciences · 2022Review
- A Fluorescent "Turn-On" Clutch Probe for Plasma Cell-Free DNA Identification from Lung Cancer Patients.Nanomaterials (Basel, Switzerland) · 2022Article
- Microsatellite instability in Chinese gastric cancer and its correlation with clinical characteristics.Journal of gastrointestinal oncology · 2021Article
- Detection of Microsatellite Instability: State of the Art and Future Applications in Circulating Tumour DNA (ctDNA).Cancers · 2021Review
Corrections and comments
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Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationMicrosatellite instability (MSI) is a promising biomarker for cancer prognosis and chemosensitivity. Techniques are rapidly evolving for the detection of MSI from tumor-normal paired or tumor-only sequencing data. However, tumor tissues are often insufficient, unavailable, or otherwise difficult to procure. Increasing clinical evidence indicates the enormous potential of plasma circulating cell-free DNA (cfNDA) technology as a noninvasive MSI detection approach.
resultsWe developed MSIsensor-ct, a bioinformatics tool based on a machine learning protocol, dedicated to detecting MSI status using cfDNA sequencing data with a potential stable MSIscore threshold of 20%. Evaluation of MSIsensor-ct on independent testing datasets with various levels of circulating tumor DNA (ctDNA) and sequencing depth showed 100% accuracy within the limit of detection (LOD) of 0.05% ctDNA content. MSIsensor-ct requires only BAM files as input, rendering it user-friendly and readily integrated into next generation sequencing (NGS) analysis pipelines. AVAILABILITY: MSIsensor-ct is freely available at https://github.com/niu-lab/MSIsensor-ct. SUPPLEMENTARY INFORMATION: Supplementary data are available at Briefings in Bioinformatics online.
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