ArticleScientific reports2015
MSIseq: Software for Assessing Microsatellite Instability from Catalogs of Somatic Mutations.
Article in Scientific reports, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 81 papers, 1 of them a synthesis that pooled it.
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Who cites it
81 citing papers in PubMed, 1 synthesis or guideline pooled it, 143 citations in OpenAlex.
- Germline and Somatic Tumor Testing in Epithelial Ovarian Cancer: ASCO Guideline.Journal of clinical oncology : official journal of the American Society of Clinical Oncology · 2020Pooled it
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- Double-base deletions and signatures associated with platinum adducts in metastatic cancer.Nucleic acids research · 2026Article
- Germline Predisposition to Oncogenic Alkylating Damage in Colorectal Cancer.Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology · 2026Article
- Diagnostic Challenges and Clinical Implications of Microsatellite Instability/Mismatch Repair Deficiency in Solid Tumors.Cancer research and treatment · 2026Review
- Identification of a large off-ladder allele of the D21S2055 locus during population genetics analysis.International journal of legal medicine · 2026Article
- Multi-omic characterization of consensus molecular subtype 1 (CMS1) colorectal cancer with dampened immune response improves precision medicine.Molecular oncology · 2025Article
- Whole genome sequencing improves tissue-of-origin diagnosis and treatment options for cancer of unknown primary.Nature communications · 2025Article
- Mercury Bioaccumulation in Female Breast Cancer Is Associated to CXCR4 Expression.International journal of molecular sciences · 2025Article
- A redefined InDel taxonomy provides insights into mutational signatures.Nature genetics · 2025Article
- The relationship between the gastric cancer microbiome and clinicopathological factors: a metagenomic investigation from the 100,000 genomes project and The Cancer Genome Atlas.Gastric cancer : official journal of the International Gastric Cancer Association and the Japanese Gastric Cancer Association · 2025Article
- Unveiling the molecular profile of a prostate carcinoma: implications for personalized medicine.Biology direct · 2024Article
- MSIsensor-RNA: Microsatellite Instability Detection for Bulk and Single-cell Gene Expression Data.Genomics, proteomics & bioinformatics · 2024Article
- Oncological characteristics, treatments and prognostic outcomes in MMR-deficient colorectal cancer.Biomarker research · 2024Review
- A comprehensive molecular characterization of a claudin-low luminal B breast tumor.Biology direct · 2024Article
- Performance assessment of computational tools to detect microsatellite instability.Briefings in bioinformatics · 2024Article
- Molecular profiling of a bladder cancer with very high tumour mutational burden.Cell death discovery · 2024Article
- Genetically driven predisposition leads to an unusually genomic unstable renal cell carcinoma.Discover oncology · 2024Article
- Genomic and transcriptomic profiling of hepatocellular carcinoma reveals a rare molecular subtype.Discover oncology · 2024Article
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21 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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.
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