Microsatellite analysis markers

A third type of polymorphism is due to tandem repeats of short sequences that can be detected by PCR-based analysis. These are known variously as microsatellites, short tandem repeats (STRs), STR polymorphisms (STRPs), or short sequence length polymorphisms (SSLPs). These repeat sequences usually consist of two, three, or four nucleotides and are plentiful in most organisms. All PCR-converted STR markers (those for which a pair of oligonucleotides flanking the polymorphic site suitable for PCR amplification of the locus has been designed) are considered to be STSs. The advent of PCR-based analysis quickly made microsatellites the markers of choice for mapping. 

By microsatellite analysis DNA fingerprints can be made from almost all mammals. Primers are published for a wide variety of mammals, birds, and fishes. For some animal species used in agriculmre, commercial PCR kits are available (Table 1.7) for other species, sets of markers are available some of which were tested in ring trials (sheep, goat, pig). In contrast to the analysis of human DNA, currentiy no aUelic ladders are commercially available for these marker sets except for porcine microsatellite analysis with a kit from Biotype. 

Microsatellites-the repeated units are typically 2-4 bp, and the length of the entire repeat is generally less than 150 bp. This dass often referred to as STRs (simple tandem repeats) is most typically amplified by a PCR for paternity testing, forensic cases, or gene linkage analysis (see Section II, Chapter 4 Polymorphic Markers and Linkage Analysis). 

Hale, A. L. (2003). Screening potato genotypes for antioxidant activity, identification of the responsible compounds, and differentiating Russet Norkotah strains using AFLR and microsatellite marker analysis, Vol. Rh.D. Texas A M University, http //handle.tamu.edU/1969.l/1602, Rh.D. Thesis, College Station. 

Figure 3 Population genetic methods used in genetic ecotoxicology to examine toxicant effects in populations of aquatic and terrestrial organisms. Methods are categorized as either co-dominant (allozymes, minisatellites, RFLP, microsatellites) or dominant (AFLP, FiAPD) markers. As shown here, techniques used to generate these markers are based on similar procedures such as PCR and electrophoresis, and similar methods of analysis, bp, base pairs.

Both FISH and PCR-based detection of LOH can be achieved successfully in FFPE samples, and each method has its own limitations. FISH will show a false-negative result in the event of uniparental disomy (i.e., when cancer cells have lost one chromosome in the presence of duplication of another chromosomal allele). The PCR-based LOH analysis can detect the Ip loss in this situation. However, for optimal performance, the PCR-LOH analysis requires normal cells (isolated from normal tissue or blood) and must rely on amplification of several markers located in the same region because some of the microsatellite loci will be non-informative. 

Eiedler W, Hoppe C, Schimmel B, et al. Molecular characterization of head and neck tumors by analysis of telomerase activity and a panel of microsatellite markers. Int J Mol Med. 2002 9(4) 417-423. 

For each of the most common genetic markers described in the previous sections, attempts have been made to develop solutions using MALDI-TOF-MS. Here, investigations involving the analysis of RFLPs [139, 140] and microsatellites [134,141-145] using MALDI-TOF-MS will be reviewed, and attention focused on those applications which have found more widespread use in genomics/genetics research. 

---