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MSIsensor specifications


Unique identifier OMICS_02192
Name MSIsensor
Software type Application/Script
Interface Command line interface
Restrictions to use None
Output data The list of microsatellites, the msi score output, the read count distribution, the somatic sites detected and the germline sites detected.
Operating system Unix/Linux
Programming languages C++
License MIT License
Computer skills Advanced
Version 0.2
Stability Stable
Maintained Yes




No version available



  • person_outline Li Ding <>
  • person_outline Kai Ye <>

Publication for MSIsensor

MSIsensor citations


Microsatellite instability in prostate cancer by PCR or next generation sequencing

PMCID: 5904988
PMID: 29665853
DOI: 10.1186/s40425-018-0341-y

[…] dna sample for every specimen assayed because rare germline polymorphisms may be misinterpreted as positive microsatellite loci. likewise, some ngs-based msi-detection methods such as mantis [] and msisensor [] require a matched-normal sample. neither msiplus nor large panel ngs require matched-normal dna, which helps to simplify testing logistics and reduce cost. 2) interpretation […]


Actionable perturbations of damage responses by TCL1/ATM and epigenetic lesions form the basis of T PLL

PMCID: 5814445
PMID: 29449575
DOI: 10.1038/s41467-017-02688-6

[…] drops of coverage. as the reference set, we pooled all germline samples obtained from the same batch of the respective tumor sample. potential microsatellite-instability (msi) was assessed using msisensor with default settings., sequential samples were compared in a pair-wise fashion: sample at f/u vs. sample at diagnosis. estimations of cellular prevalences and clustering of mutated […]


Multilevel genomics of colorectal cancers with microsatellite instability—clinical impact of JAK1 mutations and consensus molecular subtype 1

PMCID: 5442873
PMID: 28539123
DOI: 10.1186/s13073-017-0434-0

[…] for 60 of the tumors using the same analysis pipeline as for the in-house exome sequencing data., the level of msi per sample was estimated from the exome sequencing data using the algorithm msisensor [] with default settings. for a catalogue of microsatellites in the reference genome (homopolymers of a minimum of 5 base pairs and microsatellites with maximum repeat unit length 5), […]


Recurrent, truncating SOX9 mutations are associated with SOX9 overexpression, KRAS mutation, and TP53 wild type status in colorectal carcinoma

PMCID: 5239443
PMID: 27248473
DOI: 10.18632/oncotarget.9682

[…] braf (c. v600e, fusions), apc (all coding mutations), tp53 (all coding mutations), pik3ca (all coding mutations) and sox9 (all coding mutations). microsatellite instability (msi) was assessed with msisensor [] on next generation sequencing (ngs) data for cases that did not have mismatch repair (mmr) immunohistochemical (ihc) analysis for mlh1, pms2, msh2, and msh6 expression retention (mmr-p) […]


Differential clonal evolution in oesophageal cancers in response to neo adjuvant chemotherapy

PMCID: 4822033
PMID: 27045317
DOI: 10.1038/ncomms11111

[…] (γ=1,000). gains and losses were called using a logr threshold of ±0.15. these data were only used for incorporation into the pyclone program., msi was evaluated in the exome sequence data with msisensor version 0.2 (ref. ) using default parameters and filtered using a 0.05 false discovery rate threshold., accession code: the genome sequence and array data have been deposited […]


Identification of neutral tumor evolution across cancer types

PMCID: 4934603
PMID: 26780609
DOI: 10.1038/ng.3489

[…] the variant. non-crcs in the tcga had mutations called using mutect according to the pipeline described in ref. microsatellite instability in the tcga colon cancer samples was called using msisensor. annotation was performed with annovar., to fit the neutral model to allele frequency data we considered only variants with allele frequency in the range [fmax,fmin] corresponding to [t0,t] […]

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MSIsensor institution(s)
Departments of Genetics and Mathematics, The Genome Institute, Washington University in St. Louis, MO, USA; Department of Genetics, Division of Statistical Genomics, Washington University in St. Louis, MO, USA; Department of Medicine, Washington University in St. Louis, MO, USA; Siteman Cancer Center, Washington University in St. Louis, MO, USA
MSIsensor funding source(s)
Supported by National Human Genome Research Institute (U01HG006517) and National Cancer Institute (R01CA180006).

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