We can provide numbers for the sample size savings by using the mean OR for loci recently reported for schizophrenia. The mean OR for the 27 genome-wide significant loci is 1.10[1]. Assuming a population prevalence of schizophrenia of 0.7%, and assuming both the marker and disease-causing allele have a minor allele frequency of 0.3, then to achieve 80% power to detect a single locus at a 5% significance threshold (not genome-wide) we require 4,000 cases and 4,000 controls. This appears preferable to testing 32,000 (about eight times as many for a GWAS).
