We performed a meta-analysis of the individual GWAS using an inverse-weighted fixed effects model [31] implemented in METAL (http://csg.sph.umich.edu//abecasis/Metal/) [32]. A fixed effects meta-analysis was chosen over a random effects model to maximise power and improved discover of associated SNPs [33]. An additional meta-analysis was performed including 13 of the cohorts, omitting the Swedish PAGES collection, this was named noSWM3. The Swedish PAGES collection include control individuals that overlap with the PGC schizophrenia GWAS, and we wished to preclude any potential for confounding of our results which rely upon comparison of these datasets. We performed a cross-disorder meta-analysis of the noSWM3 ASD GWAS and the PGC schizophrenia GWAS [19] using an inverse-weighted fixed effects model as described above. We applied a GWS threshold of P = 5 × 10−8. This is based on the Bonferroni approach, controlling the observed associations at P = 0.05 given approximately 1000000 independent tests.
