Genome-wide association study of lifetime smoking index. For full details of genotyping and exclusion procedures see online Supplementary Note. After excluding individuals who did not pass genotype exclusions and who had missing phenotype data, 462 690 individuals remained for the GWAS. Of these individuals, 249 318 were never smokers (54%), 164 649 were former smokers (36%) and 48 723 (11%) were current smokers. The mean value of lifetime smoking score was 0.359 (s.d. = 0.694). GWAS was conducted using the UK Biobank GWAS pipeline set-up for the MRC Integrative Epidemiology Unit (Elsworth et al., 2017). BOLT-LMM was used to conduct the analysis (Loh et al., 2015), which accounts for population stratification and relatedness using linear mixed modelling. Genotyping chip and sex were included as covariates. As a sensitivity analysis, we reran the GWAS without controlling for genotype chip because the UK BiLEVE sub-sample (which used a different genotyping chip) was selected on the basis of smoking status. Genome-wide significant SNPs were selected at p < 5 × 10−8 and were clumped to ensure independence at linkage disequilibrium (LD) r2 = 0.001 and a distance of 10 000 kb using the TwoSampleMR package (Hemani et al., 2018).
