We selected unrelated individuals that passed the quality control measures according to the Gene Environment Association Studies Initiative (GENEVA) quality control report. The final number of unrelated individuals is 3,741 (1,732 male, 2,079 female) and the total number of SNP markers is 917,694. Because the purpose of our analysis is to identify the genes that are associated with addiction, we used the symptomatology variables of four highly comorbid substance use disorders as the phenotype outcomes: the number of alcohol dependence symptoms endorsed (alc_sx_tot), the number of nicotine dependence symptoms endorsed (nic_sx_tot), the number of marijuana dependence symptoms endorsed (mj_sx_tot), and the number of cocaine dependence symptoms endorsed (coc_sx_tot).
