Polygenic score analysis was conducted as described in the ISC GWAS paper (Purcell et al., 2009). We used 14,811 SNPs which were genotyped in both the ISC and SCZ GAIN samples and which mapped to candidate genes. We made a polygenic profile based on the risk alleles within these SNPs in the ISC data, and used this profile to create a polygenic score for each individual within the SCZ GAIN sample (an independent target sample). We used logistic regression between the score of each individual in SCZ GAIN and their case/control status.
