MSIsensor-pro: Fast,Accurate, and Matched-normal-sample-free Detection of Microsatellite Instability |
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| Institution: | 1. School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an 710049, China;2. MOE Key Laboratory for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an 710049, China;3. School of Computer Science and Technology, Faculty of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an 710049, China;4. School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, China;5. Leiden Institute of Advanced Computer Science, Leiden University, Leiden 2311 ZE, Netherlands;6. School of Mathematics and Statistics, Xi''an Jiaotong University, Xi''an 710049, China;7. Precision Medicine Center, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, China;8. Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA;9. Genome Institute, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, China |
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| Abstract: | Microsatellite instability(MSI) is a key biomarker for cancer therapy and prognosis. Traditional experimental assays are laborious and time-consuming, and next-generation sequencingbased computational methods do not work on leukemia samples, paraffin-embedded samples, or patient-derived xenografts/organoids, due to the requirement of matched normal samples. Herein,we developed MSIsensor-pro, an open-source single sample MSI scoring method for research and clinical applications. MSIsensor-pro introduces a multinomial distribution model to quantify polymerase slippages for each tumor sample and a discriminative site selection method to enable MSI detection without matched normal samples. We demonstrate that MSIsensor-pro is an ultrafast,accurate, and robust MSI calling method. Using samples with various sequencing depths and tumor purities, MSIsensor-pro significantly outperformed the current leading methods in both accuracy and computational cost. MSIsensor-pro is available at https://github.com/xjtu-omics/msisensor-pro and free for non-commercial use, while a commercial license is provided upon request. |
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| Keywords: | Microsatellite Polymerase slippage Multinomial distribution Microsatellite instability Tumor |
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