Numerous methods have been developed for SNP genotyping (for review, see Kwok, 2001; Sobrino et al., 2005). The methods all employ one of four common technologies: hybridization, primer extension, ligation or invasive cleavage. For forensic applications, single base extension (SBE) is currently the preferred method (Figure 6.2), because it is highly accurate and can be performed with the same instruments used for STR analyses (polymerase chain reaction machines and electrophoresis instruments). The SBE reaction is performed as consecutive cycles of denaturation of double-stranded DNA, annealing of the SBE primers to the polymerase chain reaction (PCR) products and single base extension. The SBE primer anneals to the single-stranded PCR product immediately upstream of the SNP position, and the DNA polymerase adds a fluorescently labelled dideoxyri-bonucleotide, complementary to the nucleotide in the SNP position, to the SBE primer. Single base extension reactions can be multiplexed and many SBE products
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