A limitation of functional genomics studies in Alzheimer’s disease is the lack of well–powered QTL data for microglia, which are probably the most relevant disease-affected cell type on the basis of SNP heritability.38 No large QTL datasets exist for human microglia, leading investigators to use QTL datasets for peripheral myeloid cells. Additionally, most QTL datasets are generated under baseline conditions, but some functional variants might be dependent on intrinsic or extrinsic factors not present under baseline conditions. As a result, the inability to assign functional variants or causal genes might be due to the absence of annotations in disease–relevant conditions.
