the mean arctan A/B ratio for abusers (or quitters) by the mean arctan A/B ratio for controls (or nonquitters) to form abuser/control (or quitter/nonquitter) ratios. We generated a "t" statistic for the differences between abusers and controls or quitters and nonquitters using the formula described previously [22,31,55]. "Nominally significant" SNPs display t values with p < 0.005 for nicotine dependent vs control comparisons and p < 0.01 for quitter vs nonquitter comparisons, respectively. We thus set a relatively strict preplanned criterion for the first comparison that confirms genes with good confidence. We set a more modest criterion, with lower levels of confidence, for the second comparison that nominates genes that merit replication studies. We deleted data from SNPs on sex chromosomes and SNPs whose chromosomal positions could not be adequately determined using Mapviewer (NCBI, build 35.1) or NETAFFYX (Affymetrix, Santa Clara, CA).
