Another limitation of GWA studies is that the markers identified are often not the causal variants themselves, but rather, are in linkage disequilibrium with them. This may contribute to the lack of reproducibility between studies as these markers may be in linkage disequilibrium in one population but not another. Furthermore, causal variants may not be well tagged by SNPs used in commercial genotyping arrays. This highlights the importance of identifying functional genetic predictors involved in complex diseases such as drug addiction.
