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Architecture of pharmacogenomic associations: structures with functional foundations or castles made of sand?

In the construction of any building, a foundation beneath the surface is required to ensure that the structure has a stable footing and is serviceable. Just like a building, a pharmacogenomic association requires a foundation. In this case, a foundation can be constructed from the elucidation of the genetic mechanism behind the pharmacogenomic association, providing a supportive biological basis. If the function of the genetic variant believed to provide the association (which we will call ‘associated SNP’ for simplicity) is not known, it is difficult to make a biological interpretation and determine whether the causal variant has been identified [1]. Consequently, establishing a functional foundation is a crucial step in the validation of any pharmacogenomic association and even more so when the ability to conduct external replication is limited. This is particularly a problem of pharmacogenomic studies stemming from clinical trials of experimental drugs, as independent study cohorts will very likely not exist. In these instances, the establishment of a functional foundation is an essential part in the process of demonstrating clinical validity and utility.