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Figure 5.6 Genotyping at 15 microsatellite (STR) loci via multiplex PCR and capillary electrophoresis using the AmpFlSTR® identifier kit. The genotype was determined by GeneMapper® software. The upper set of numbers located beneath the peaks indicate the number of alleles and the lower set indicate the peak intensity

Figure 5.6 Genotyping at 15 microsatellite (STR) loci via multiplex PCR and capillary electrophoresis using the AmpFlSTR® identifier kit. The genotype was determined by GeneMapper® software. The upper set of numbers located beneath the peaks indicate the number of alleles and the lower set indicate the peak intensity

NPA has taken initiative in implementing this system in its forensic applications since 2006.

In situations where a direct comparison between evidence and a suspect is being made, mutation rates are an insignificant issue. However, with comparisons between relatives in parentage testing and kinship analysis - such as victim identification in mass disasters - mutational events may lead to false negatives (Biesecker et al., 2005). In comparison to minisatellites, the mutation rate in most microsatellites is much lower, 0.2% at the most. Consequently, microsatellites are better suited for paternity testing as long as a greater number of loci are used compared with minisatellites, in order to compensate for the relatively low level of polymorphism at each locus.

In recent years the development of commercialized kits has reduced what once was a painstaking task into a simple procedure. Since its inception, these kits have achieved new heights in quality and the microsatellite systems commercially available today have a high standard of sensitivity. Unfortunately, the forensic specimens that we encounter in the field are often degraded or fragmented. As a result, when amplification of DNA is attempted at loci yielding relatively long PCR products (e.g. CSF1PO, D2S1338, D18551 and FGA in Figure 5.6), we often fail to retrieve any PCR products, making it impossible to determine the genotypes of these particular loci. To remedy this situation, innovative PCR techniques known as 'mini-STRs' are currently being developed (Butler et al., 2003), which involve bringing primer annealing sites closer to the microsatellites in order to shorten the PCR products, and selecting loci with relatively short allele length distributions,. Recently, two different parallel strategies have emerged in Europe. The first employs a 13-STR loci multiplex incorporating three mini-STRs into the currently used multiplex test. The second strategy employs a multiplex of six high-molecular-weight STRs (also in current use), modified to provide smaller amplicons with an additional two loci of high discriminating power. Eventually, the two strategies will merge to provide a single multiplex of 15 STR loci (Gill et al., 2006). In this section, we have addressed the applications of autosomal microsatellites; however, microsatellites in the Y chromosome (YSTRs) are of equal importance and should not be ignored (see Chapter 9). Detailed information on forensic microsatellites can be obtained at STRBase (Ruitberg et al., 2001).

In the future, technological advances, along with newer and more improved methods, may give rise to an alternative typing platform utilizing SNPs. This could greatly accelerate typing and offers the potential for DNA analysis to be conducted at the scene of crime. However, even with the introduction of an alternative typing platform, the multiplex microsatellite markers employed today will remain in use for the time being, primarily because millions of DNA profiles - such as those contained in national databases - were generated with STR loci and will require ongoing maintenance.

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