The cost effectiveness of duplicate genotyping for testing genetic association

We consider a modification to the traditional genome wide association (GWA) study design: duplicate genotyping. Duplicate genotyping (re-genotyping some of the samples) has long been suggested for quality control reasons; however, it has not been evaluated for its statistical cost-effectiveness. We demonstrate that when genotyping error rates are at least m%, duplicate genotyping provides a cost-effective (more statistical power for the same price) design alternative when relative genotype to phenotype/sample acquisition costs are no more than m%. In addition to cost and error rate, duplicate genotyping is most cost-effective for SNPs with low minor allele frequency. In general, relative genotype to phenotype/sample acquisition costs will be low when following up a limited number of SNPs in the second stage of a two-stage GWA study design, and, thus, duplicate genotyping may be useful in these situations. In cases where many SNPs are being followed up at the second stage, duplicate genotyping only low-quality SNPs with low minor allele frequency may be cost-effective. We also find that in almost all cases where duplicate genotyping is cost-effective, the most cost-effective design strategy involves duplicate genotyping all samples. Free software is provided which evaluates the cost-effectiveness of duplicate genotyping based on user inputs.