log(OR)s/beta coefficients. For each trait, we calculated risk scores at 5 P-value thresholds: 5 × 10−5, 5 × 10−4, 5 × 10−3, 5 × 10−2 and 5 × 10−1. The numbers of markers used to calculate schizophrenia risk scores at these thresholds were 6,014, 94,804, 268,070, 1,021,476 and 5,370,899. The numbers of markers used for FTND and COT were 731, 6,312, 55,378, 500,542 and 4,752,196; and 1,621, 6,357, 48,575, 473,100, and 4,737,313 respectively. We then tested whether schizophrenia risk scores predicted FTND scores and vice versa using logistic (schizophrenia) and linear regression (FTND scores). Since the number of cigarettes smoked per day (CPD) was available from the FTND datasets, we also tested whether the genetic risk scores for schizophrenia predicted the CPD phenotype. Because we did not have individual genotypes for all datasets used in the COT meta-analyses, we used only the COT risk score to predict schizophrenia diagnosis. Sex, age and study were included as covariates in regression analyses.
