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MSIsensor-pro: Fast, Accurate, and Matched-normal-sample-free Detection of Microsatellite Instability

Microsatellite instability (MSI) is a key biomarker for cancer therapy and prognosis. Traditional 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...

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Detalles Bibliográficos
Autores principales: Jia, Peng, Yang, Xiaofei, Guo, Li, Liu, Bowen, Lin, Jiadong, Liang, Hao, Sun, Jianyong, Zhang, Chengsheng, Ye, Kai
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7393535/
https://www.ncbi.nlm.nih.gov/pubmed/32171661
http://dx.doi.org/10.1016/j.gpb.2020.02.001
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author Jia, Peng
Yang, Xiaofei
Guo, Li
Liu, Bowen
Lin, Jiadong
Liang, Hao
Sun, Jianyong
Zhang, Chengsheng
Ye, Kai
author_facet Jia, Peng
Yang, Xiaofei
Guo, Li
Liu, Bowen
Lin, Jiadong
Liang, Hao
Sun, Jianyong
Zhang, Chengsheng
Ye, Kai
author_sort Jia, Peng
collection PubMed
description Microsatellite instability (MSI) is a key biomarker for cancer therapy and prognosis. Traditional 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 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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spelling pubmed-73935352020-08-04 MSIsensor-pro: Fast, Accurate, and Matched-normal-sample-free Detection of Microsatellite Instability Jia, Peng Yang, Xiaofei Guo, Li Liu, Bowen Lin, Jiadong Liang, Hao Sun, Jianyong Zhang, Chengsheng Ye, Kai Genomics Proteomics Bioinformatics Method Microsatellite instability (MSI) is a key biomarker for cancer therapy and prognosis. Traditional 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 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. Elsevier 2020-02 2020-03-12 /pmc/articles/PMC7393535/ /pubmed/32171661 http://dx.doi.org/10.1016/j.gpb.2020.02.001 Text en © 2020 The Authors http://creativecommons.org/licenses/by/4.0/ This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Method
Jia, Peng
Yang, Xiaofei
Guo, Li
Liu, Bowen
Lin, Jiadong
Liang, Hao
Sun, Jianyong
Zhang, Chengsheng
Ye, Kai
MSIsensor-pro: Fast, Accurate, and Matched-normal-sample-free Detection of Microsatellite Instability
title MSIsensor-pro: Fast, Accurate, and Matched-normal-sample-free Detection of Microsatellite Instability
title_full MSIsensor-pro: Fast, Accurate, and Matched-normal-sample-free Detection of Microsatellite Instability
title_fullStr MSIsensor-pro: Fast, Accurate, and Matched-normal-sample-free Detection of Microsatellite Instability
title_full_unstemmed MSIsensor-pro: Fast, Accurate, and Matched-normal-sample-free Detection of Microsatellite Instability
title_short MSIsensor-pro: Fast, Accurate, and Matched-normal-sample-free Detection of Microsatellite Instability
title_sort msisensor-pro: fast, accurate, and matched-normal-sample-free detection of microsatellite instability
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7393535/
https://www.ncbi.nlm.nih.gov/pubmed/32171661
http://dx.doi.org/10.1016/j.gpb.2020.02.001
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