Single Nucleotide Polymorphisms And Other Biallelic Markers

Research into the identification and validation of more and better marker systems for forensic analysis should continue with a view of making each profile unique.

(NRC II Report, p. 7. Recommendation 5.3)


In this chapter and the next two, we will examine other DNA markers that are being used or being developed for forensic DNA typing purposes. The 13 core loci described in Chapter 5 are being extensively used today and will probably continue to be used for many years in the future because they are part of the DNA databases that are growing around the world. Yet forensic DNA scientists often use additional markers as the need arises to obtain further information about a particular sample (see Gill et al. 2004).

Sex-typing is performed in conjunction with available short tandem repeat (STR) kits to provide the gender of the individual who is the source of the DNA sample in question. Additionally, in cases where samples may be extremely degraded and fail to result in useful information with conventional STR typing, mitochondrial DNA (see Chapter 10) may be used because it is in higher copy number per cell than nuclear DNA and thus more resistant to complete sample degradation.

Y chromosome systems are becoming more popular as a means to extract information from the male portion of a sample mixture (e.g., evidence in rape cases). In Chapter 9, we include a brief review of new Y chromosome STR markers that are being used to provide additional information in forensic DNA analysis. Information from non-human DNA sources (see Chapter 11) has already been used to solve forensic cases and will continue to grow in value as our knowledge of genomic DNA sequence diversity from human populations as well as other organisms improves.

It is conceivable that within a few years, a wide variety of validated marker sets and technologies will exist that will provide a forensic DNA laboratory with a smorgasbord of possibilities in their arsenal of weapons that may be used to solve crimes with biological evidence. In this chapter, we concentrate on a class of genetic markers known as single nucleotide polymorphisms (SNPs) that have received a lot of attention in recent years due to their abundance throughout the human genome.


A single base sequence variation between individuals at a particular point in the genome is often referred to as a single nucleotide polymorphism or SNP. SNPs are abundant in the human genome and as such are being used for linkage studies to track genetic diseases (Brookes 1999). Millions of SNPs exist per individual. The abundance of SNPs means that they will likely play a role in the future of differentiating individuals from one another. Table 8.1 compares and contrasts SNP and STR markers. A number of technologies are being developed to miniaturize and automate the procedure for SNP analysis. For example, a microchip-based SNP assay has been described where more than a thousand SNPs were examined simultaneously (Wang et al. 1998).

Table 8.1

Comparison of STR and SNP markers. SNPs are more common in the human genome than STRs but are not as polymorphic.

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