We did separate association analyses for each sample (ie, 18 individual samples from Psychiatric Genomics Consortium, iPSYCH, and deCODE) by ancestry. For the eight case-control studies from the Psychiatric Genomics Consortium, imputed dosages were analysed using logistic regression models, implemented in the Ricopili pipeline.13 For family-based samples of the Psychiatric Genomics Consortium, we did association analyses with imputed best-guess genotypes using generalised estimating equations for samples that included only first-degree relatives (eg, sibships), and logistic mixed models for complex pedigrees, in the Picopili pipeline.7 For calculation of SNP heritability and genetic correlations, subsets of genetically unrelated individuals were selected from each family-based sample from the Psychiatric Genomics Consortium and analysed using logistic regression through Picopili (5289 cases, 10 004 controls). These results were then meta-analysed along with the case-control groups. Psychiatric Genomics Consortium covariates included sex and five to ten within-ancestry principal components to account for population stratification (appendix pp 12–13). Because age was not available in all samples, it was not included as a covariate in the Psychiatric Genomics Consortium analyses. Sensitivity analyses in one representative sample showed this to have no impact on study-specific findings.
