The final array design included 646,247 markers: 296,038 genome-wide association markers; 255,862 tag SNPs and 17,632 exonic markers in addiction-related gene regions; 11,099 fine-mapping markers in loci related to nicotine metabolism and smoking behavior; and the remaining markers in other categories (Table 1; markers in categories have some overlap). Coverage estimates are provided using the number of variants available through genotype imputation in the 1000 Genomes Project Phase 1 [49] Yoruba in Ibadan, Nigeria (YRI), East Asian (ASN), and European (EUR) populations (Table 2).Table 1Smokescreen genotyping array contentCategoryMarkersa 1014 addiction-related genes Tag SNPs (MAF ≥ 0.05)255862 Exonic markers17632 Genome-wide association markers Affymetrix’ Axiom® Biobank GWAS grid246038 African (YRI) booster panel50000 Fine-mapping of smoking related loci CHRNA5-CHRNA3-CHRNB4 (552 kb LD block)8913 CYP2A6 (±20 kb)573 CYP2B6 (±20 kb)1613 High-value addiction markers NeuroSNP Project4994 Pharmacogenetics of Nicotine Addiction Treatment (PNAT) SNP panels2271 v1.0 Quit Success Score12058 Literature search1329 Comorbidity markers Lung Cancer3091 Psychiatric disorders1200 Tobacco smoke constituent update and metabolic phenotypes1907 Pulmonary diseases and traits7945 Cardiovascular diseases and traits2247 General high-value markers Pharmacogenomic markers2030 NHGRI GWAS Catalog7612 eQTLs9736 Loss-of-function markers4680 Ancestry informative markers
