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mSINGS specifications

Information


Unique identifier OMICS_20469
Name mSINGS
Alternative name MSI by NGS
Software type Application/Script
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input data A sample of interest aligned against reference genome, with the locations of the microsatellite tracts of interest.
Input format BAM, FASTA, BED
Output data The distribution of alleles of differing length.
Output format TXT
Operating system Unix/Linux
Programming languages Perl, Python, Shell (Bash)
Computer skills Advanced
Version 3.1
Stability Stable
Requirements
Numpy
Maintained Yes

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Maintainers


  • person_outline Colin Pritchard <>
  • person_outline Sheena Scroggins <>

Publication for MSI by NGS

mSINGS citations

 (4)
library_books

Microsatellite instability in prostate cancer by PCR or next generation sequencing

2018
PMCID: 5904988
PMID: 29665853
DOI: 10.1186/s40425-018-0341-y

[…] ngs see additional file : table s1, for coordinates of the loci captured by large-panel ngs see additional file : table s1, msi was assessed from broca or uw-oncoplex sequence data [, ] using msings as previously described by salipante et al. []. this method evaluates microsatellite loci that are incidentally captured during targeted sequencing of gene panels (146 mononucleotide […]

library_books

Comprehensive population wide analysis of Lynch syndrome in Iceland reveals founder mutations in MSH6 and PMS2

2017
PMCID: 5418568
PMID: 28466842
DOI: 10.1038/ncomms14755

[…] possibly solved if only one pathogenic or likely pathogenic mutation was identified with possible loh. phenotypic msi was assessed with coloseq tumour next-generation sequencing data using msings (msi by ngs)., one microgram tumour dna was treated with sodium bisulphite using the ez methylation gold kit (zymo research, irvine, california), according to the manufacturer's instructions. […]

library_books

Mismatch repair deficiency may be common in ductal adenocarcinoma of the prostate

2016
PMCID: 5347709
PMID: 27756888
DOI: 10.18632/oncotarget.12697

[…] tissue was submitted for dna extraction. uw-oncoplex was performed according to previously published methods []. microsatellite instability (msi) testing was performed directly on ngs data using the msings method []. total mutation burden was estimated from targeted ngs data as previously described, with hypermutation defined as > 12 mutations/megabase []., we thank all the men who generously […]

library_books

Complex MSH2 and MSH6 mutations in hypermutated microsatellite unstable advanced prostate cancer

2014
PMCID: 4176888
PMID: 25255306
DOI: 10.1038/ncomms5988

[…] of individual exons using custom perl scripts. cnv plots were visualized using the r package ggplot2., phenotypic msi was assessed directly from broca next-generation sequencing data using msings (msi by ngs). this method evaluated up to 146 mononucleotide microsatellite loci that are captured by broca in both matched normal non-tumour and tumour samples. for each specimen, […]


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mSINGS institution(s)
Department of Laboratory Medicine, University of Washington, Seattle, WA, USA; Department of Internal Medicine, Division of Human Genetics, The Ohio State University, Columbus, OH, USA
mSINGS funding source(s)
Supported by 2013 Young Investigator Award from the Prostate Cancer Foundation.

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