We integrated results from a meta-analysis of 18 SCZ GWASs with existing informative SCZ databases to select SNPs for a family-based replication study. Results suggested a considerable enrichment of small P values in the replication study. Test results showed that this enrichment was statistically significant. Furthermore, of the SNPs with replication values of P<.01, the proportion of SNPs that had the same direction of effect as in the GWAS meta-analysis was about 90%, which is almost impossible to occur by chance. Finally, analyses suggested several significant pathways, which again suggested that SNPs replicated. Because the group of selected SNPs replicated as a whole, it follows that individual SNPs in the replication study replicate. A complication was that rather than a few SNPs having large effects, many SNPs appeared to have small effects. Although our pathway analyses of these SNPs implicated specific pathogenic processes, some caution is required before making strong statements about the replication status of individual SNPs. Other studies have reached a similar conclusion that for SCZ, many SNPs with small effects may be involved and these SNPs replicate
