A comparison between SNaPshot, pyrosequencing, and biplex invader SNP genotyping methods: accuracy, cost, and throughput

Three methods of Single Nucleotide Polymorphism (SNP) detection: SNaPshot, Pyrosequencing and Biplex Invader, with two different chemistries were investigated to compare, (1) accuracy, (2) ease of use, (3) throughput capability, and (4) cost. We genotyped 192 human DNA samples across 24 SNPs (minor allele frequencies above 30%), of which seven SNPs were genotyped with all three methods. We show that the Biplex Invader genotyping method was found to be the most accurate and easiest to use with lowest cost, although Pyrosequencing provided similar results at a low cost. With little optimization, the accuracy of the SNaPshot method was also comparable to these two methods with a higher cost, if only singleplex reactions are used.