We applied a permutation based approach in order to evaluate how the inclusion and exclusion of individuals with CUD affected the association of our index variant rs56372821 with schizophrenia. The analyses were based on the iPSYCH sample consisting of 2,281 schizophrenia cases and 23,134 population based controls (genotyping, QC and imputation were done using the same procedures as explained above). Odds ratios were obtained by the glm() function in R using dosage data from the imputed SNP rs56372821, and including principle components PC1-PC4 and PCs signicantly associated with SZ and/or CUD and genotyping wave as covariates.
