Short, interspersed nuclear elements (SINEs) are another form of repeated DNA that has been investigated for population variation studies. SINEs consist of a short, identifiable sequence inserted at a location in the genome. The best studied SINEs are Alu insertion polymorphisms, which were named for an AluI
restriction endonuclease site typical of the sequence. Alu units are found in nearly one million copies per haploid genome (5-10% of the human genome) and can be found flanking genes or clustered with other interspersed repeated sequences (Primrose 1998).
The insertion of an Alu element at a particular locus can be regarded as a unique event. Once inserted, Alu elements are stable genetic markers and do not appear to be subject to loss or rearrangement. Human-specific Alu insertions may be typed in a bi-allelic fashion by using PCR, agarose gel electrophoresis, and ethidium bromide staining (Batzer et al. 1993). The presence of the Alu insertion will be indicated by a 400 bp PCR product while the absence of the insertion will result in a 100 bp amplicon (Figure 8.3). Commonly used Alu insertion polymorphisms include APO, PV92, TPA25, FXIIIB, D1, ACE, A25, and B65 (Sajantila 1998).
Alu repeats have shown the potential to yield information about the geographic/ethnic origin of the sample being tested (Batzer et al. 1993, Bamshad et al. 2003). Since many Alu sequences are unique to humans (Batzer and Deininger 1991), it may be possible to design multiplex assays that are completely human-specific (i.e., no cross-reaction with even other primates). However, Alu repeats exhibit less variation than multiplex STR profiles and would therefore most likely be used to gain more information on an unknown sample rather than as an independent source of identification.
Figure 8.3 Schematic of the Alu element insertion PCR assay. The Alu sequence, which is approximately 300 bp in size, may either be present or absent at a particular location in the human genome. When the flanking region of the Alu repeat is targeted with primers, PCR amplification will result in products that are 400 bp ifthe Alu element is inserted or 100 bp if it is absent. A simple ethidium bromide-stained agarose gel may be used to genotype individuals. Individuals that are homozygous for the insertion will amplify a 400 bp DNA fragment. Those who are heterozygous for the insertion will amplify both 400 bp and 100 bp fragments, and individuals that are homozygous for the lack of the Alu insertion element will exhibit only the 100 bp DNA fragment.
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