In summary, we see the most important results here as methodological. We have developed and tested a network based approach to clarifying the genetic substrate of complex diseases. Applying this to a pre-selected set of candidate genes genotypes in cases with AD and controls, we found evidence that variants in four neurotransmitter pathways (norepinephrine, glutamate, GABA, and CRH) significantly contributed to risk for AD. These results are broadly consistent with the prior literature and suggest that network analyses may be a useful addition to the more standard approaches to clarifying the genetic basis of complex disorders, especially when prior biological hypothesis of disease etiology can lead to predicted gene pathways.