There are three limitations that should be considered when drawing conclusions from this work. First, none of the p-values have been corrected for multiple testing of different phenotypes. These data have been previously examined for nicotine dependence (Saccone et al., in press), and it is probable that the data may be analyzed to examine other related phenotypes in the future. Likewise, we chose to analyze SNPs in the CHRNB3 gene separately from the CHRNA6 gene, based on previous work that had specifically implicated the CHRNB3 gene (and our own functional work). However, by doing this, the overall gene significance level of CHRNB3 may be slightly inflated. Finally, although the functional data provide evidence for differences in gene expression, it will be important to elucidate the possible mechanism of differences (e.g. transcriptional or post-transcriptional) in future studies. Likewise, it will be important to determine whether such differences correspond to differences in protein levels, but these experiments are limited currently by the fact that there is no method for specifically measuring Chrnb3 protein, since no reliable antibodies are available.
