Indeed, many of the pathways indicated in our analysis of the breast cancer data (Table 2) were not detected using SNP-set enrichment [17]–[19] (data not shown), including the highly significant purine metabolism and GnRH signaling pathways, both of which are biologically relevant (purine metabolism has been implicated in cancers generally due to its role in DNA and RNA synthesis [40], and GnRH has been shown to be clinically important in breast and gynecological cancers [53]). This evidence concerns the gene GNRH1 and female reproductive organ cancer.