Besides performing analyses for millions of genetic variants across the genome, one may also analyze thousands of phenotypes of interest for association with these variants. “Phenome scans” superimposed on GWA scans can yield interesting new discoveries, but they also add an extra dimension of multiplicity of comparisons. One should clarify whether one is searching agnostically a large number of phenotypes or is focusing on a specific type of phenotype(s). For phenome scan-derived associations, typical levels of “genome-wide statistical significance” used for single-phenotype analyses [16] may not be sufficient. If data are selectively available only for the “winner” phenotypes, even a meticulous meta-analysis can yield misleading conclusions. Finally, sometimes there may exist multiple analytical options for the same data (e.g. different genetic models, use or not of different adjustments, and so forth) [17].
