We compared two genome-wide association studies of smoking behavior to evaluate the importance of phenotype in genome-wide association studies. We found SNPs on chromosome 8 in the region of CHRNB3 that reached genome-wide significance in their association with nicotine dependence, but did not reach genome-wide significance in the GWAS using CPD as a dependent variable. Interestingly, the association was stronger in our combined sample of 4,200(p=6.7×10−16), than in the meta-analysis of CPD with a combined sample of over 75,000 subjects (p=1.3×10−8)(15).We attribute this discrepancy to the use of an FTCD-based definition of nicotine dependence rather than CPD.
