MSIsensor-pro:Fast, Accurate, and Matched-normal-sample-free Detection of Microsatellite Instability
- Author:
Jia PENG
1
;
Yang XIAOFEI
;
Guo LI
;
Liu BOWEN
;
Lin JIADONG
;
Liang HAO
;
Sun JIANYONG
;
Zhang CHENGSHENG
;
Ye KAI
Author Information
1. School of Automation Science and Engineering
- Keywords:
Microsatellite;
Polymerase slippage;
Multinomial distribution;
Microsatellite instability;
Tumor
- From:
Genomics, Proteomics & Bioinformatics
2020;18(1):65-71
- CountryChina
- Language:Chinese
-
Abstract:
Microsatellite instability (MSI) is a key biomarker for cancer therapy and prognosis. Tra-ditional experimental assays are laborious and time-consuming, and next-generation sequencing-based 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 poly-merase 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 accuracyand 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.
