THE DEVELOPMENT OF STR MULTIPLEXES
THO1 – Simple repeat with a non-consensus allele
Figure 6.1 The structure of three commonly used STR loci, THO1, FGA and D21S11. The THO1 locus has a simple repeat with a non-consensus allele; in the example the 9.3 allele is missing an A from the seventh repeat∗. The FGA locus is a compound repeat composed of several elements. The D21S11 allele is an example of a complex repeat; the three regions not included in the FGA nomenclature are an invariant TA, TCA and TCCATA sequence. ∗The AATG nomenclature is commonly used but breaks the adopted conventions for STR nomenclature as it represents the bottom strand of the first sequence described in GenBank.
In addition to STR loci, the amelogenin locus which is present on the X and Y chromosomes has been incorporated into all commonly used STR multiplex kits. The amelogenin gene encodes for a protein that is a major component of tooth enamel matrix; there are two versions of the gene, the copy on the X chromosome has a 6 bp deletion and this length polymorphism allows the versions of the gene on the X and Y chromosomes to be differentiated (Figure 6.2) .
Figure 6.2 The amelogenin locus is present on both the X and Y chromosomes. The gene that is present on the X chromosome has a 6 bp deletion. The primers (schematically shown by the arrowed lines) that were reported by Sullivan et al. (1993)  lead to products of 106 bp from the X chromosome and 112 bp from the Y chromosome