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Updated: Nov 21, 2025
Detection and Monitoring of Tumor Associated Circulating DNA in Patient Biofluids
Published on: June 8, 2019
MSIsensor-ct: microsatellite instability detection using cfDNA sequencing data
Xinyin Han1,2, Shuying Zhang1,2, Daniel Cui Zhou3,4
1Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China.
Motivation:
Microsatellite 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.
Results:
We 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.
