Short tandem repeat polymorphisms

Forensic analysis of DNA samples DNA fingerprinting by means of PCR has revolutionized the analysis of evidence from crime scenes. DNA isolated from a single human hair, a tiny spot of blood, or a sample of semen is sufficient to determine whether the sample comes from a specific individual. The DNA markers analyzed for such fingerprinting are most commonly short tandem repeat polymorphisms (STRs). These are very similar to the VNTRs described previously (see p. 455), but are smaller in size. [Note Verification of paternity uses the same techniques.]... 

There are several major types of DNA sequence variation in the human genome. One type comprises repeated sequences with variations in the number of repeat units, such as short tandem repeat polymorphisms (STRPs, also known as microsatellites) in the form of mono-, di-, tri-, and tetra-nu-cleotide repeats, or more complex sequence repeats such as variable number tandem repeats (VNTRs) [2-4]. Repeat polymorphisms are relatively... 

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Getting W S, et al. (1995). Linkage analysis with multiplexed short tandem repeat polymorphisms using infrared fluorescence and M13 tailed primers. Genomics. 30(3) 450-458. 

Hahner, S., Schneider, A, Ingendoh, A., and Mosner, J. (2000) Analysis of short tandem repeat polymorphisms by electrospray ion trap mass spectrometry. Nudeic Acids Res., 28,18. 

Ross, P.L. and Belgrader, P. (1997) Analysis of short tandem repeat polymorphisms in human DNA by matrix-assisted laser desorption/ ionization mass spectrometry. Anal. Chem., 69 (19), 3966-3972. 

Biomolecular MS and in particular MALDI-TOF-MS (see Sections 2.1.22 and 2.2.1) permit the routine analysis of oligonucleotides up to 70-mers, intact nucleic acids, and the direct detection of DNA products with no primer labels with an increase in analysis speed and mass accuracy especially in contrast to traditional DNA separation techniques such as slab gels or capillary electrophoresis. Applications focus on the characterization of single nucleotide polymorphisms (SNPs) and short tandem repeats (STRs). Precise and accurate gene expression measurements show relative and absolute numbers of target molecules determined independently of the number of PCR cycles. DNA methylation can be studied quantitatively. 

H. Oberacher, W. Parson, R. Milhlmann, C.G. Huber, Analysis of PCR products by on-line LC-MS for genotyping of polymorphic short tandem repeat loci. Anal. Chem., 73 (2001)5109. 

Badano JL, Inoue K, Katsanis N, Lupski JR. New polymorphic short tandem repeats for PCR-based Charcot-Marie-Tooth disease type lA dupfication diagnosis. Clin Chem 2001 47 838-43. 

Latour P, Boutrand L, Levy N, Bernard R, Boyer A, Claustrat F, et al. Polymorphic short tandem repeats for diagnosis of the Charcot-Marie-Tooth disease lA duplication. Clin Chem 2001 47 829-37. 

This amounts to 4 x 10 differences in the whole genome. In addition to these single nucleotide polymorphisms (SNPs) there are many differences in the >100,000 nearly randomly dispersed short tandem repeats of microsatellite The latter form... 

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. 

Butler, J., Recent developments in Y-short tandem repeat and Y-single nucleotide polymorphism analysis. Forensic Sci Rev, 15, 91, 2003. 

Figure 1 Schematic presentation of the DNA from two individuals and zoom on a region of their DNA to show that DNA is a linear molecule made of nucleotides, and to illustrate the two main types of polymorphisms used in forensics the short tandem repeats (STRs) and the single nucleotide polymorphisms (SNPs).

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