Microsatellite repeat markers

Microsatellite repeat markers—Highly polymorphic DNA sequences of short repeats generally comprising <6... 

FIGURE 2.15 Detection of microsatellite instability using the NCI recommended panel of five microsatellite markers. In this colon cancer sample, all five markers show microsatellite instability, which manifests as change in size of microsatellite repeats seen on capillary gel electropherograms of tumor PCR products. Electropherograms of normal tissue PCR products are used as a negative control. 

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. 

Microsatellite markers have been extensively used in family studies. These are regions of variation, mostly (CA) repeats, which are distributed throughout the genome. There are potentially as many as 105 loci, each of which has many alleles and these markers are, therefore, highly informative. Microsatellites can be typed by automated multiplex PCR. 

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). 

AGTAGTAGTAGTAGT... ), etc. Due to polymerase slip (a.k.a. polymerase chatter), during DNA replication there is a slight chance these repeat sequences may become altered copies of the repeat unit can be created or removed. Consequently, the exact number of repeat units may differ between unrelated individuals. Considering all the known microsatellite markers, no two individuals are identical. This is the basis for forensic DNA identification and for testing of familial relationships (e.g., paternity testing). 

Microsatellite loci exhibit significant variability and stability, resulting from a high rate of mutation, which may have important consequences in evolution (Sia et al., 1997 Young et al., 2000). Further, not all tandem repeats are polymorphic. As such, care must be taken in using these markers as the basis of relatedness. 

---