Due to the duplicated, palindromic regions of the Y chromosome mentioned above, some Y-STR loci occur more than once and when amplified with a locus-specific set of primers produce more than one PCR product. This fact can lead to some confusion in terms of counting the number of loci present in a haplo-type. A single set of primers can produce two amplicons, which may be thought of as 'two loci' for a Y chromosome haplotype.
For example, the Y-STR locus DYS385 is present in two regions along the long arm of the Y chromosome. These duplicated regions are located about 40 000 bp apart and can generate two different alleles when amplified with a single set of primers. The two alleles are typically labeled 'a' and 'b' with the 'a' designation going to the smaller sized allele. It is also possible to have both 'a' and 'b' alleles be the same size in which case only a single peak would appear in an electropherogram (see Figure 9.5a). Due to the presence of two alleles, this duplicated locus is usually referred to as DYS385 a/b. It has been recently demonstrated that with a nested PCR approach, the 'a' and 'b' alleles for DYS385 can be amplified separately (Kittler et al. 2003, Seo et al. 2003). Other multi-copy Y-STRs besides DYS385 a/b that have been used in human identity testing include YCAIIa/b and DYS464 a/b/c/d (Redd et al. 2002, Butler 2003, Schoske et al. 2004).
Two PCR products can also be generated at the DYS389 locus with a single set of primers. However in this case the DYS389I PCR product is a subset of the
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