(TTTTT)-primerl (chromosome 20)-ddT/ddT (TTTTT)-(TTTTT)-primer2 (chromosome 6)-ddC/ddT (TTTTT)-(TTTTT)-(TTTTT)-primer3 (chromosome 14)-ddC/ddT (TTTTT)-(TTTTT)-(TTTTT)-(TTTTT)-primer4 (chromosome 1)-ddC/ddC

The color of a peak in a minisequencing assay conveys the nucleotide present at the SNP site of interest while the size position of a peak correlates back to its locus based on the 5'-tailing used to differentiate the SNP marker from its neighbors. Homozygous alleles appear as single peaks and heterozygous alleles as two adjacent peaks (Figure 8.2). Automated allele designation can be performed with computer programs such as Genotyper or GeneMapper designed to look for peaks in a particular color and size range.

A major advantage of allele-specific primer extension is that samples can be run on multi-color fluorescence detection electrophoresis instrumentation already available in most forensic DNA typing laboratories (e.g., ABI 310, 377, 3100; see Chapter 14). The technique is sensitive (Vallone et al. 2004), has the ability to be multiplexed (Tully et al. 1996, Sanchez et al. 2003), and has proven to be fairly robust with casework samples (Morley et al. 1999, Vallone et al. 2004).


Several potential applications of SNPs exist for human identity testing. These center around three areas: estimating ethnic origin of a sample, predicting physical traits of a perpetrator, and recovering more information from a degraded DNA sample.

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