Gene set and pathway analyses of GWAS data are potentially powerful tools that have made several contributions to our understanding of the genetics of AD. The analyses summarized here have nominated novel candidate genes for AD and have highlighted pathways of potential importance. Although gene set and pathway analyses are leverage GWAS data to gain mechanistic insight into the biology of complex traits, they are analytically limited, failing to capture alternative transcripts of genes, providing incomplete and inaccurate annotations, and lacking information on the role of pathways in specific cell types and under specific conditions (Khatri et al., 2012). The recently completed ENCODE project (ENCODE Project Consortium, 2012), a major source of new information that may greatly increase our knowledge and understanding of biological pathways, will likely contribute to the improvement of currently available methods. Thus, pathway and related analyses are likely to become increasingly important approaches to gene finding for AD.
