Most of the SNPs assessed by these commercial microarrays were chosen in ways that are not based on hypotheses about the underlying biology of any particular disorder. However, to the extent that there is a body of knowledge concerning the biology of a disorder, not all genes may be as likely, a priori, to contain disease associated variants. Thus, if a commercial microarray is used for a GWAS, we might ask – how well does the microarray cover biologically relevant genes for which there is a priori reason to believe their products are involved in the disease of interest [3]? For example, because genes that encode nicotinic cholinergic receptors have a clear biochemical connection to nicotine dependence, as do alcohol dehydrogenases for alcoholism, we should be especially vigilant in testing the hypothesis that variants in these genes might influence addiction vulnerability.
