xia1yang/msisensor

microsatellite instability detection using tumor only or paired tumor-normal data

Note: For questions and discussion about msisensor, please visit the repository of msisensor-pro at https://github.com/xjtu-omics/msisensor-pro.

MSIsensor

MSIsensor is a C++ program to detect replication slippage variants at microsatellite regions, and differentiate them as somatic or germline. Given paired tumor and normal sequence data, it builds a distribution for expected (normal) and observed (tumor) lengths of repeated sequence per microsatellite, and compares them using Pearson's Chi-Squared Test. Comprehensive testing indicates MSIsensor is an efficient and effective tool for deriving microsatellite instability (MSI) status from standard tumor-normal paired sequence data. MSIsensor is publiched in Bioinformatics. Please click here to see more details about MSIsensor. If you have any questions about MSIsensor, please contact one or more of the following folks: Beifang Niu ([email protected]), Kai Ye ([email protected]) or Li Ding ([email protected]).

If you use these tools for your work, please cite the following papers:
[1] Niu, B. et al. MSIsensor: microsatellite instability detection using paired tumor-normal sequence data. Bioinformatics 30, 1015-1016, doi:10.1093/bioinformatics/btt755 (2014).
[2] Jia, P. et al. MSIsensor-pro: Fast, Accurate, and Matched-normal-sample-free Detection of Microsatellite Instability. Genomics, Proteomics & Bioinformatics, doi:https://doi.org/10.1016/j.gpb.2020.02.001 (2020).

MSIsensor-pro is a new MSI detection method developed by Kai Ye et al. MSIsensor-pro is a fast, accurate, and matched-normal-sample-free MSI detection method. It accepts the whole genome sequencing, whole exome sequencing and target region (panel) sequencing data as input. MSIsensor-pro introduces a multinomial distribution model to quantify polymerase slippages for each tumor sample and a discriminative sites selection method to enable MSI detection without matched normal samples. MSIsensor-pro is now published in Genomics Proteomics & Bioinformatics. If you have any question about MSIsensor-pro, please open a issue on MSIsensor-pro's homepage or contact with Kai Ye ([email protected]) directly.

MSIsensor2 is also a MSI detecteion method specially designed for tumor only sequencing data. MSIsensor2 was developed by Beifang Niu's lab ([email protected]) independently. Please try the MSIsensor2 here: https://github.com/niu-lab/msisensor2 or require any further details here: http://niulab.scgrid.cn/msisensor2/index.html.