Though the typing of restriction fragment length polymorphisms (RFLPs) was originally the primary method of DNA forensic analysis, the main forensic DNA analysis method of today uses autosomal short tandem repeat (STR) loci, which are usually typed by multiplex polymerase chain reaction (PCR) methods. The profiles from an STR multiplex analysis are displayed in a computer-generated
Molecular Forensics. Edited by Ralph Rapley and David Whitehouse Copyright 2007 by John Wiley & Sons, Ltd.
graph called an electropherogram. The sources of ambiguity of an electrophero-gram profile are mixtures of samples, degradation of DNA, allelic drop-out, spurious peaks (technical artefacts) or false peaks.
In selected cases, such as degraded samples or when very small amounts of the sample are available for study, 'mini' STR markers that use shorter ampli-cons (Biesecker et al., 2005), autosomal single nucleotide polymorphisms (SNPs) or markers on the mitochondrial DNA or on the Y chromosome are more useful (Jobling and Gill, 2004). The two largest DNA databases in the world, the UK National DNA Database (>3.4 million profiles) and the USA DNA database (>3.5 million profiles), use multiplex autosomal STR methods. Because SNPs have much lower heterozygosities than STRs, data from a larger number of SNP loci would be required to obtain the same discrimination potential. There is currently a 21-locus autosomal SNP multiplex that has been introduced (Dixon et al., 2005).
In rape cases there may be a mixing of the victim's DNA and the rapist's DNA in the vaginal vault or other anatomical locations. Differential lysis is a technique used for vaginal fluid/semen mixtures that concentrates the sperm by lysing the victim's epithelial cells. This process thus eliminates the masking of the rapist's DNA by the victim's DNA. Though first described in 1985 (Jeffreys et al., 1985b), the original protocol is still used today.
Autosomes (nuclear DNA)
Currently, the most common method for forensic analysis of nuclear DNA is to use a multiplex system for STRs (see Chapter 5). There are about 20 000 known STR loci, however about 20 select loci are used in most forensic cases (DNA Advisory Board, 2000). The STRs that are commonly used were selected because they are independent: that is, the inheritance of one locus does not influence the inheritance of another locus. The 13 core loci used by the US FBI CODIS system are: TPOX, D3S1358, FGA, D5S818, CSF1PO, D7S820, D8S1179, TH01, VWA, D13S317, D18S51, D21S11 and D16S539 (Budowle et al., 1998) Along with these 13 core loci, the amelogenin locus for sex determination is also examined (Sullivan et al., 1993). For each locus, a genotype for the sample will be identified; then the frequency of such a genotype can be calculated using population genotypes. An example of this process is presented later in this chapter, using the loci in Table 12.1.
At times the SNP approach may be utilized for nuclear DNA analysis, instead of the more popular (and discriminating) STRs, because SNPs are more useful in analysing degraded DNA than are STRs.
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