Genotype imputation was conducted in each non-isolated sample using IMPUTE2 (ref. 25) with reference to the 1000 Genomes ALL phase I integrated variant set.25,26 Additional details are provided in the Supplementary Information. Following imputation and removal of SNPs and insertions/deletions (indels) with minor allele frequency <0.01 in the 1000 Genomes EUR panel (collection of five European-ancestry populations), we tested 8 548 225 SNPs and 1 395 199 indels for association with nicotine dependence across the samples. We used the info metric to evaluate the SNP/indel imputation quality rather than imposing an imputation quality filter and possibly missing truly associated SNPs/indels.27 The SNP and indel genotype probabilities were converted to dosages and used in the regression model for association testing with nicotine dependence to account for any imputation uncertainty.28
