Example use of PoolingPlanner. Power curves for a theoretical pooling experiment with 300 cases and 1000 controls where 24, 12, 6, or 3 Illumina 660-Quad replicate arrays are used to allelotype the DNA pools. The equivalent individual genotyping experiment is given for reference. Effective sample size assuming 24, 12, 6, or 3 arrays was calculated using PoolingPlanner (see Table 2) and these values entered into Quanto  to obtain pool-adjusted estimates of power over a range of odds ratios. Calculations are based on an unmatched case-control design testing for gene-only effects using a log-additive model, where the incidence of the case phenotype is 0.02%, and the risk allele frequency (prisk) is 29% (and in complete linkage disequilibrium with a SNP on the array). A dashed line is draw to indicate the 80% power threshold.
Earp et al. BMC Medical Genomics 2011 4:81 doi:10.1186/1755-8794-4-81