![]() ![]() Waalkes A, Smith N, Penewit K, Hempelmann J, Konnick EQ, Hause RJ, Pritchard CC, Salipante SJ (2018) Accurate pan-cancer molecular diagnosis of microsatellite instability by single-molecule molecular inversion probe capture and high-throughput sequencing. Zhang S, Niu Y, Bian Y, Dong R, Liu X, Bao Y, Jin C, Zheng H, Li C (2018) Sequence investigation of 34 forensic autosomal STRs with massively parallel sequencing. Le DT, Durham JN, Smith KN, Wang H, Bartlett BR, Aulakh LK, Lu S, Kemberling H, Wilt C, Luber BS, Wong F, Azad NS, Rucki AA, Laheru D, Donehower R, Zaheer A, Fisher GA, Crocenzi TS, Lee JJ, Greten TF, Duffy AG, Ciombor KK, Eyring AD, Lam BH, Joe A, Kang SP, Holdhoff M, Danilova L, Cope L, Meyer C, Zhou S, Goldberg RM, Armstrong DK, Bever KM, Fader AN, Taube J, Housseau F, Spetzler D, Xiao N, Pardoll DM, Papadopoulos N, Kinzler KW, Eshleman JR, Vogelstein B, Anders RA, Diaz LA Jr (2017) Mismatch repair deficiency predicts response of solid tumors to PD-1 blockade. Zeinalian M, Hashemzadeh-Chaleshtori M, Salehi R, Emami MH (2018) Clinical aspects of microsatellite instability testing in colorectal cancer. Wimmer K, Kratz CP, Vasen HF, Caron O, Colas C, Entz-Werle N, Gerdes AM, Goldberg Y, Ilencikova D, Muleris M, Duval A, Lavoine N, Ruiz-Ponte C, Slavc I, Burkhardt B, Brugieres L (2014) Diagnostic criteria for constitutional mismatch repair deficiency syndrome: suggestions of the European consortium ‘care for CMMRD’ (C4CMMRD). Umar A, Boland CR, Terdiman JP, Syngal S, de la Chapelle A, Ruschoff J, Fishel R, Lindor NM, Burgart LJ, Hamelin R, Hamilton SR, Hiatt RA, Jass J, Lindblom A, Lynch HT, Peltomaki P, Ramsey SD, Rodriguez-Bigas MA, Vasen HF, Hawk ET, Barrett JC, Freedman AN, Srivastava S (2004) Revised Bethesda guidelines for hereditary nonpolyposis colorectal cancer (Lynch syndrome) and microsatellite instability. Hause RJ, Pritchard CC, Shendure J, Salipante SJ (2016) Classification and characterization of microsatellite instability across 18 cancer types. ![]() Mirkin SM (2007) Expandable DNA repeats and human disease. īoland CR, Goel A (2010) Microsatellite instability in colorectal cancer. ![]() Gettings KB, Aponte RA, Vallone PM, Butler JM (2015) STR allele sequence variation: current knowledge and future issues. Miah G, Rafii MY, Ismail MR, Puteh AB, Rahim HA, Islam KN, Latif MA (2013) A review of microsatellite markers and their applications in rice breeding programs to improve blast disease resistance. Stadele V, Vigilant L (2016) Strategies for determining kinship in wild populations using genetic data. Putman AI, Carbone I (2014) Challenges in analysis and interpretation of microsatellite data for population genetic studies. Gulcher J (2012) Microsatellite markers for linkage and association studies. Capillary electrophoresis fragment analysisĮllegren H (2004) Microsatellites: simple sequences with complex evolution.In this chapter, we describe in detail all the experimental steps necessary for the development of LT-RPA simplex and multiplex assays for microsatellite genotyping and MSI detection, including the design, optimization, and validation of the assays combined with capillary electrophoresis or NGS. LT-RPA greatly simplifies the genotyping of microsatellites and improves the detection of MSI in cancer. In this context, the recently developed low-temperature recombinase polymerase amplification (LT-RPA) is an isothermal DNA amplification method at low temperature (32 ☌) that drastically reduces and sometimes completely abolishes the formation of stutter peaks. However, their amplification during PCR generates undesirable frameshift products known as stutter peaks caused by polymerase slippage, complicating data analysis and interpretation, while very few alternative methods for microsatellite amplification have been developed to reduce the formation of these artifacts. The standard analytical method for microsatellite analysis relies on PCR amplification followed by capillary electrophoresis or, more recently, next-generation sequencing (NGS). Microsatellites are short tandem repeats of one to six nucleotides that are highly polymorphic and extensively used as genetic markers in numerous biomedical applications, including the detection of microsatellite instability (MSI) in cancer.
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