Abstract
Microsatellites, also known as STRs (short tandem repeats), are tandem repeats of a simple dinucleotide, trinucleotide, tetranucleotide, pentanucleotide, or hexanucleotide sequence (two to six bases) that occur abundantly and at random throughout most eukaryotic genomes (roughly one microsatellite every 10 kb). They are typically short (often less that 100 bp long) and embedded within unique sequence, thus being ideal for designing flanking primers for in vitro amplification by the polymerase chain reaction (PCR) (see Chapter 6). The high degree of polymorphism, as a result of variation in the number of repeat units, and the stability displayed by microsatellites make them perfect markers for use in constructing high-resolution genetic maps to identify susceptibility loci involved in common genetic diseases (1). In addition to their applications in genome mapping and positional cloning, these markers have been applied in fields as diverse as tumor biology, personal identification, population genetic analysis, and the construction of human evolutionary trees. To appreciate the impact that microsatellite analysis has had within the medical field, search PubMed for “microsatellite” on the National Center for Biotechnology Information website www.ncbi.nlm.nih.gov and thousands of entries will be found. References can be found that date back more than 20 yr. Today, microsatellites are still being used extensively to investigate the genome although rapid advances in technology have seen many modifications to the original methods.
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References
Koreth, J., O’Leary, J. J., and McGee, J. (1996) Microsatellites and PCR genomic analysis. J. Pathol. 178(3), 239–248.
Lee, W.-H., Bookstein, R., Hong, F., Young, L.-J., Shew, J.-Y., and Lee, E. Y. (1987) Human retinoblastoma susceptibility gene: cloning, identification and sequencing. Science 235, 1394–1399.
Jones, M. H. and Nakamura, Y. (1992) Detection of loss of heterozygosity at the human TP53 locus using a dinucleotide repeat polymorphism. Genes Chromosomes Cancer 5(1), 89–90.
Kinzler, K. W. and Vogelstein, B. (1996) Lessons from hereditary colorectal cancer. Cell 87, 159–170.
Burton, M. P., Schneider, B. G., Brown, R., Escamilla-Ponce, N., and Gulley, M. L. (1998) Comparison of Histologic stains for use in PCR analysis of microdissected, paraffin-embedded tissues. BioTechniques 24, 86–92.
Pabst, T., Schwaller, J., Tobler, A., and Fey, M. F. (1996) Detection of microsatellite markers in leukaemia using DNA from archival bone marrow smears. Br. J. Haematol. 95, 135–137.
Huang, Q., Choy, K. W., Cheung, K. F., Lam, D. S., Fu, W. L., and Pang, C. P. (2003) Genetic alterations on chromosome 19, 20, 21, 22, and X detected by loss of heterozygosity analysis in retinoblastoma. Mol. Vis. 9, 502–507.
Ibbotson, R. E. and Corcoran, M. M. (2001) Detection of Chromosomal Deletions by Microsatellite Analysis, in Molecular Analysis of Cancer (Boultwood, J. and Fidler, C., eds.), Humana, Totowa, NJ, pp. 59–65.
Arzimanoglou, II., Gilbert, F., and Barber, H. R. (1998) Microsatelllite instability in human solid tumours. Cancer 82, 1808–1820.
Goggins, M. et al. (1998) Pancreatic adenocarcinomas with DNA replication errors (RER+) are associated with wild-type K-ras and characteristic histopathology. Poor differentiation, a syncytial growth pattern, and pushing borders suggest RER+. Am. J. Pathol. 152, 1501–1507.
Takanishi, D. M., Jr. et al. (1995) Chromosome 17p allelic loss in colorectal carcinoma. Clinical significance. Arch. Surg. 130, 585–589.
Kato, M., Ito, Y., Kobayashi, S., and Isono, K. (1996) Detection of DCC and Ki-ras gene alterations in colorectal carcinoma tissue as prognostic markers for liver metastatic recurrence. Cancer 77, 1729–1735.
Chen, X. Q., Stroun, M., Magnenat, J. L., et al. (1996) Microsatellite alterations in plasma DNA of small cell lung cancer patients. Nature Med. 2, 1033–1035.
Nawroz, H., Koch, W., Anker, P., Stroun, M., and Sidransky, D. (1996) Microsatellite alterations in serum DNA of head and neck cancer patients. Nature Med. 2, 1035–1037.
Spafford, M. F., Koch, W. M., Reed, A. L., et al. (2001) Detection of head and neck squamous cell carcinoma among exfoliated oral mucosal cells by microsatellite analysis. Clin. Cancer Res. 7(3), 607–612.
Mao, L. et al. (1996) Molecular detection of primary bladder cancer by microsatellite analysis. Science 271, 659–662.
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© 2005 Humana Press Inc., Totowa, NJ
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Ibbotson, R.E., Parker, A.E. (2005). Microsatellite Analysis. In: Walker, J.M., Rapley, R. (eds) Medical Biomethods Handbook. Springer Protocols Handbooks. Humana Press. https://doi.org/10.1385/1-59259-870-6:463
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DOI: https://doi.org/10.1385/1-59259-870-6:463
Publisher Name: Humana Press
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