In the design of such studies two fundamental decisions have to be made: which loci to genotype, and in how many individuals. Both decisions have practical constraints. For example it is currently not possible to assay all known variation in the human genome at a reasonable cost and choices must be made between a set of commercially available genotyping chips. Similarly, sample sizes are often limited by the number of well characterized clinical samples. Therefore, ultimately, the researcher and funding bodies must ask how to use the financial and practical resources available in order to best further the understanding of the genetics of the disease or trait of interest. A primary consideration should be the power of the study: the probability of detecting a variant assumed to be causal.
