Each cohort was analyzed separately for each of the 3 phenotypes considered. The majority of the analysis was carried out on the raw genotype data in Oxford but some cohorts (SardiNIA, VIS, KORCULA, ORCADES, SHIP) carried out their own analysis and submitted results for the meta-analysis. For the binary traits (Ever/Never, Current/Non-Current) tests for additive genetic effects on the logodds scale were carried out using logistic regression. For the categorical SQ phenotype, tests for additive genetic effects were carried out on a linear scale using linear regression. The programs SNPTEST, probABEL and MERLIN were used on the various cohorts to fit these models taking account of the genotype uncertainty at imputed SNPs. All tests conditioned on Sex and Age and for some cohorts other covariates of self-reported ancestry, country of origin or PCA-derived covariates were included (a complete list is given in Supplementary Table 1). A Genomic Control (GC) lambda estimate was calculated for each phenotype and each cohort (Supplementary Table 3).
