6 The analysis of short tandem repeats
Short tandem repeats were first used in forensic casework in the early 1990s [1-3]. By the end of the decade they had become the standard tool for just about every forensic laboratory in the world. Today the vast majority of forensic genetic casework involves the analysis of STR polymorphisms and this situation is unlikely to change in the near future .
Structure of STR loci
Short tandem repeats contain a core repeat region between 1 and 6 bp long and have alleles that are generally less than 350 bp long. A large number of STR loci have been characterized  but only around 20 are commonly analysed in forensic casework (Table 6.1). pair core-repeat motif and can be classified as a simple repeat, simple repeat with non-consensus repeats, compound repeat or complex repeat  (Figure 6.1).
The development of STR multiplexes
The forensic community has selected STR loci to incorporate into multiplex reactions based on several features including:
*discrete and distinguishable alleles;
*amplification of the locus should be robust;
*a high power of discrimination;
*an absence of genetic linkage with other loci being analysed;
*low levels of artefact formation during the amplification (see Chapter 7);
*the ability to be amplified as part of a multiplex PCR.
Table 6.1 generation multiplex (SGM) were developed by the Forensic Science Service in the UK. The AmpFlSTR® SGM Plus® became commercially available in 1999 and has been adopted by a large number of laboratories for routine forensic casework. The AmpFlSTR® Identifiler® and PowerPlex® 16 both analyse 15 STR including the 13 loci CODIS loci that are required to be analysed for forensic casework in the USA. The two kits are used widely worldwide, particularly for kinship testing
An essential feature of any STR used in forensic analysis is that biological material should give an identical profile regardless of the individual or laboratory that carries out the analysis. Without this standardization it would not be possible to compare results between laboratories and developments like national DNA databases would not be possible [7-11]. All new multiplexes have to be vigorously validated before they are used for the analysis of casework [12-19]. In the UK the Forensic Science Service (FSS) developed the first STR-based typing system that was designed for forensic analysis. Four STR loci were amplified in the same reaction [20-22]. This was replaced by the SGM (second generation multiplex) that was also developed by the FSS [23-25]. Two commercial companies, Applied Biosystems and Promega Corporation, have developed a series of multiplexes that are now used by most laboratories. The AmpFlSTR® SGM Plus® that is produced by Applied Biosystems replaced the SGM in the UK and has been adopted by many other countries around the world as one of their standard multiplex kits . In the USA, STR technology was adopted into forensic casework following a survey of 17 previously characterized STR loci and in 1997 13 loci were selected as the CODIS (Combined DNA Index System) loci [8, 26]. These loci can be analysed in one PCR using one of two commercially available kits; the AmpFlSTR® Identifiler® produced by Applied Biosystems  and the PowerPlex® 16 produced by Promega Corpo- ration . The STR loci that are incorporated into different multiplexes are shown in Table 6.1.