There are now multiple tools available that allow assessing epigenetic variation across the genome, based on modification of methylated DNA or chromatin immunoprecipitation and microarray hybridization methods (ChIP-chip), the latter now being replaced by modern high throughput sequencing methods (ChIP-seq, see Figure 3) (48) (49, 50). These tools, when appropriately applied to complex disorders, will likely lead to significant new discoveries of the mechanisms of disease, like they have for cancer. Many of the same problems encountered in GWGE studies also need to be considered here, including the differences between tissues and cell types that could mask differences or confound results. Additional complexity is added by the many different types of histone modification one needs to examine to obtain a thorough epigenetic assessment. Yet, however many the complexities, the promise is great, especially as pharmacological agents that can affect epigenetic modifications are already available (51).
