Significant SNP disadvantages
Several significant disadvantages exist with SNP markers when considered as a possible replacement for currently used STR loci with the top two being the number of loci needed and the inability to easily decipher mixtures. First, because SNPs are not as polymorphic as STRs, more SNPs are required to reach equivalent powers of discrimination or random match probabilities. Numbers on the order of 40–60 SNPs have been suggested in order to approximate the power of 13–15 STR loci as are commonly in use today [10, 12, 19].
Remember that 15 STRs can be routinely amplified simultaneously in a single multiplex amplification reaction from minimal amounts (e.g., 500 pg) of DNA template using commercially available kits such as PowerPlex 16 and Identifiler. While multiplex PCR amplification of such a large number of SNPs (e.g., *50) has only recently been demonstrated in a research setting [14], routine production and commercialization of robust assays containing upwards of 100 oligonucleotide PCR primers will not be trivial. Likewise, the expense of examining more loci will be higher.
Perhaps more importantly data interpretation becomes increasingly difficult with more loci and amplification products. Issues with locus drop out will become more significant when three to five times more loci are involved in comparison to traditional STR typing. In addition, assays with a larger number of loci are more sensitive to the quantity and integrity of the input DNA template particu- larly when trying to amplify limited DNA materials.