We applied SSEA to two large genetically distinct GWAS data sets for schizophrenia from the Genetic Association Information Network (GAIN, http://www.genome.gov/19518664) studies [25], available at the database of Genotype and Phenotype (dbGaP) [26]. The study version we reported here is phs000021.v2.p1 with general research use consent, which includes two samples; one is from the European American (EA) ancestry and the other one is from African American (AA) ancestry. Individuals in those two cohorts represent two genetically distinct populations [27,28]. However, we should note that the two data sets were collected and quality controlled in a similar way, which might affect the independence of the two data sets. Both samples were genotyped by the Affymetrix SNP array 6.0. With GAIN quality-control criteria and after removing redundant subjects, the data sets included 1172 cases and 1378 controls in EA and 921 cases and 954 controls in AA. Since Linkage Disequilibrium (LD) is an important concern for selecting representative SNPs for each gene, we used Plink http://pngu.mgh.harvard.edu/~purcell/plink/ to prune SNPs that are in strong LD (Plink uses 0.5 as the default pairwise R2
