MSIseq: Software for Assessing Microsatellite Instability from Catalogs of Somatic Mutations View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2015-10

AUTHORS

Mi Ni Huang, John R McPherson, Ioana Cutcutache, Bin Tean Teh, Patrick Tan, Steven G Rozen

ABSTRACT

Microsatellite instability (MSI) is a form of hypermutation that occurs in some tumors due to defects in cellular DNA mismatch repair. MSI is characterized by frequent somatic mutations (i.e., cancer-specific mutations) that change the length of simple repeats (e.g., AAAAA…., GATAGATAGATA...). Clinical MSI tests evaluate the lengths of a handful of simple repeat sites, while next-generation sequencing can assay many more sites and offers a much more complete view of their somatic mutation frequencies. Using somatic mutation data from the exomes of a 361-tumor training set, we developed classifiers to determine MSI status based on four machine-learning frameworks. All frameworks had high accuracy, and after choosing one we determined that it had >98% concordance with clinical tests in a separate 163-tumor test set. Furthermore, this classifier retained high concordance even when classifying tumors based on subsets of whole-exome data. We have released a CRAN R package, MSIseq, based on this classifier. MSIseq is faster and simpler to use than software that requires large files of aligned sequenced reads. MSIseq will be useful for genomic studies in which clinical MSI test results are unavailable and for detecting possible misclassifications by clinical tests. More... »

PAGES

13321

References to SciGraph publications

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/srep13321

DOI

http://dx.doi.org/10.1038/srep13321

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1030209182

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/26306458


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