Schizophrenia risk scores were calculated for 9 independent smoking related studies (Table S1, n = 10,794) with FTND and CPD measures using the summary statistics from the PGC schizophrenia meta-analysis. The control subjects from the Molecular Genetics of Schizophrenia (MGS) were included in the GWASs of both FTND and PGC schizophrenia, therefore they were excluded from this analysis. Risk scores for COT and FTND were calculated for 13,326 individuals from the NIMH genetics consortium repository (https://www.nimhgenetics.org/). We estimated the risk scores for each trait using the algorithms implemented in the PLINK software70. Specifically, the risk score for an individual was the sum of the number of risk alleles multiplied by the logarithm of odds ratio (OR, for schizophrenia) or beta coefficient (for FTND and COT), which was then normalized subsequently by the product of maximal number of risk alleles and 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
