Many limitations, potential pitfalls and confounding factors must be considered when interpreting the information provided by GWGE studies. Unlike analyzing constitutional DNA which is expected to be almost identical across cell types and tissues (with the notable exception of tumors), the source of RNA is a defining parameter in GWGE studies. Different tissues and different cell types have distinctly different expression profiles and likely involve different regulatory mechanisms. Solid tissues contain multiple cell types that are hard to separate and, although techniques like laser capture microdissection (41) have been developed for this purpose, their use in large-scale gene expression studies is not always practical. As a result, one must be aware that the observed expression profile is often the summation from more than one cell type and in certain cases (for example in the brain in neurodegenerative disorders) the relative cell type abundance might differ between cases and controls. Further, the acquisition of some types of tissues (for example, brain) is almost entirely limited to postmortem specimens, introducing additional confounding parameters like the cause of death and the delay in
