distribution for the odds ratio was generated by performing 10,000 permutations randomly removing 556 and 101 individuals among the cases and controls, respectively (Supplementary Figure 1). The observed odds ratio for rs56372821, when excluding individuals with comorbid CUD was 0.97, and differed significantly from random removal of the same number of cases and controls (Ptwo-sided=0.0027, Pone-sided=0.0015). Thus the permutation test supports the hypothesis that the subgroup diagnosed with CUD among schizophrenia cases drives the nominal association observed for rs56372821 in the iPSYCH schizophrenia sample.
