Figure 5.5 An example of alignable MS32 alleles. The ethnic origin (R: j, Japanese; ch, Chinese; th, Thai) and MVR code of a- and t-type repeats are shown for each allele. Haplotypic MVR map segments shared by related alleles are shown in uppercase and divergences by lowercase. Gaps (-) have been introduced to improve alignments. Some alleles show uncertain positions (?) and the unknown haplotypes of long alleles beyond the mapped region are indicated by (. . .)
units of 1-5 bp typically repeated 5-30 times. Most microsatellite loci can be efficiently amplified by standard PCR since the repeat regions are shorter than 100 bp. Some microsatellites can display substantial polymorphism - though far less than at the most variable minisatellites - and are found abundantly throughout the human genome, which contains over a million of these loci (International Human Genome Sequencing Consortium, 2001). Microsatellites are particularly suitable for analysing forensic specimens containing degraded and/or limited amounts of DNA. The first forensic application of microsatellites involved typing the skeletal remains of a murder victim (Hagelberg et al., 1991), followed by the identification of Josef Mengele, the Auschwitz 'Angel of Death' (Jeffreys et al., 1992). Although the spurious shadow or stutter bands often observed at dinucleotide repeat loci can make interpretation difficult, small PCR products can be sized with precision by polyacrylamide gel electrophoresis (PAGE). Because interpretation can sometimes be difficult, current typing systems employ the use of microsatellites with repeat units 4 bp long to minimize problems of stuttering. The microsatellite approach allows very high throughput via multiplex PCR (single-tube PCR reactions that amplify multiple loci) and fluorescent detection systems have been developed to allow substantial automation of gel or capillary electrophoresis and DNA profile interpretation (Edwards et al., 1991).
Microsatellite analysis is highly sensitive and can even recover information from a single cell. Discrete allele sizes, combined with automated electrophoresis and interpretation, make unambiguous assignment of alleles possible. For these reasons, the USA, most European nations and numerous other countries have established ever-growing databases. In the United Kingdom, 10 autosomal STR loci plus the amelogenin sex test, typed using the 'second-generation multiplex' (SGM) Plus system, are used in forensic practice (Table 5.1; Tamaki and Jeffreys, 2005). The SGM Plus loci generate random match probabilities of typically 10-11 between two unrelated individuals in the three UK racial groups (Caucasian, Afro-Caribbean and Asian) (Foreman and Evett, 2001). The US FBI CODIS (Combined DNA Index System) uses 13 STRs plus amelogenin. These loci produce extremely low random match probabilities. For example, around 60% of Japanese individuals show match probabilities of 10-14-10-17 (estimates from Yoshida et al., 2003, and Hayashida et al., 2003). In 2003, the Japanese National Police Agency (NPA) introduced a nine-microsatellite locus system, which uses some CODIS loci (the AmpFlSTR® Profiler® kit), for analysing forensic specimens. From allele frequencies at these nine loci (Yoshida et al., 2003), around 60% of Japanese individuals have match probabilities of 10-910-11. This particular system also detects X-Y homologous amelogenin genes to reveal the sex of a sample. Recently, new multiplexes that amplify 16 loci in a single reaction, including amelogenin, have been commercially developed (Figure 5.6). These systems produce even lower match probabilities without sacrificing sensitivity, and it is likely that such systems will remain the standard for analysing specimens in both forensic applications and paternity tests. The Japanese
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