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Microsatellite instability identification software tools | High-throughput sequencing data analysis

Microsatellite instability (MSI) is a form of hypermutation caused by defective DNA mismatch repair (MMR). MSI is characterized by widespread changes in the length of genomic mononucleotide repeats (e.g., AAAAA….) or microsatellites (e.g., GATAGATAGATA….), collectively termed simple repeats (Iacopetta et al., 2010; Boland et al., 1998; Eshleman and Markowitz, 1996). MSI is also characterized by high rates of single-nucleotide-substitution (SNS) mutations (Greenman et al., 2007). MSI can arise due to germ-line mutations in MMR genes, due to somatic mutations in MMR genes, or due to epigenetic inactivation of MMR genes (Veigl et al., 1998; Cunningham et al., 1998).

References:
(Iacopetta et al., 2010) Microsatellite instability in colorectal cancer. Asia Pac J Clin Oncol.
(Boland et al., 1998) A National Cancer Institute Workshop on Microsatellite Instability for cancer detection and familial predisposition: development of international criteria for the determination of microsatellite instability in colorectal cancer. Cancer Res.
(Eshleman and Markowitz, 1996) Mismatch repair defects in human carcinogenesis. Hum Mol Genet.
(Greenman et al., 2007) Patterns of somatic mutation in human cancer genomes. Nature.
(Veigl et al., 1998) Biallelic inactivation of hMLH1 by epigenetic gene silencing, a novel mechanism causing human MSI cancers. Proc Natl Acad Sci U S A.
(Cunningham et al., 1998) Hypermethylation of the hMLH1 promoter in colon cancer with microsatellite instability. Cancer Res.

Source text:
(Huang et al., 2015) MSIseq: Software for Assessing Microsatellite Instability from Catalogs of Somatic Mutations. Sci Rep.

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