The ISC GWAS had 3,322 cases, 3,587 controls, and 1,948,385 genotyped and imputed autosomal SNPs. The sample size was 1.36 times greater than the largest hypothesis-driven candidate gene study. Statistical power was 89% to detect a genetic effect corresponding to that typical for SNPs implicated in human disease GWAS (Hindorff et al., 2009) including adjustment for multiple comparisons (α=5×10−8). The ISC reported 1,948,385 associations, which exceeds the total associations in the SZGene database by over 180-fold. The mean marker density over the genome was 1 SNP/1.6 kb. In comparison to HapMap (r27, phases I+II+III), ISC markers assessed 79.0% of known common variants present in individuals of European ancestry either directly or indirectly with r2 ≥ 0.8.
