In practice, we do not know which are the true causal genotypes for a trait, so we have to select a set of SNPs to use in our PRS. Often, the data we have at our disposal for selecting SNPs are derived from a genotyping platform that did not interrogate all sequence genotypes, but rather a reduced set of a few million (or fewer) variants. For PRS construction, we often have only a set of associated genotypes that likely tag a subset of the causal genotypes.
