We tested for SNP associations with schizophrenia with a logistic regression model using the PLINK software [26] and including sex and curated EIGENSTRAT axes as covariates. An additive genetic model was tested. A series of quality control procedures were undertaken before this analysis (for details see Text S1). The results were then annotated using the WGAViewer software [27]. No single polymorphism showed a genome-wide significant association in the discovery cohort. The top 100 associated SNPs are shown in Table 1. The most strongly associated SNPs at this stage were in the ADAMTSL3 gene (lowest p = 1.34×10−6, Table 1).
