MSIsensor statistics

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Citations per year

Number of citations per year for the bioinformatics software tool MSIsensor
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Tool usage distribution map

This map represents all the scientific publications referring to MSIsensor per scientific context
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Associated diseases

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Popular tool citations

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Protocols

MSIsensor specifications

Information


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

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Documentation


Maintainers


  • person_outline Li Ding
  • person_outline Kai Ye

Publication for MSIsensor

MSIsensor citations

 (3)
library_books

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

2018
Nat Commun
PMCID: 5814445
PMID: 29449575
DOI: 10.1038/s41467-017-02688-6

[…] cant 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 population […]

library_books

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

2017
Genome Med
PMCID: 5442873
PMID: 28539123
DOI: 10.1186/s13073-017-0434-0

[…] mors (average 2.94, standard deviation 0.25; Additional file : Table S5). An MSI score representing the percentage of somatically unstable microsatellites per tumor was calculated using the algorithm MSIsensor (Fig. ; Additional file : Table S5). The MSI score was strongly correlated with the number of indels per tumor, as expected, but only weakly associated with the number of SNVs (Spearman corr […]

call_split

Identification of neutral tumor evolution across cancer types

2016
Nat Genet
PMCID: 4934603
PMID: 26780609
DOI: 10.1038/ng.3489
call_split See protocol

[…] supporting 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] in […]


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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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