Pathway-Based GWAS Analysis
I am a big fan of pathway-based approaches to the analysis of GWAS data. This looks like a nice overview. This area needs more attention and is much more likely to pay off than the one-SNP-at-a-time approach that has dominated the field.
Wang K, Li M, Hakonarson H. Analysing biological pathways in genome-wide association studies. Nat Rev Genet. 2010 Dec;11(12):843-854. [PubMed]
Genome-wide association (GWA) studies have typically focused on the analysis of single markers, which often lacks the power to uncover the relatively small effect sizes conferred by most genetic variants. Recently, pathway-based approaches have been developed, which use prior biological knowledge on gene function to facilitate more powerful analysis of GWA study data sets. These approaches typically examine whether a group of related genes in the same functional pathway are jointly associated with a trait of interest. Here we review the development of pathway-based approaches for GWA studies, discuss their practical use and caveats, and suggest that pathway-based approaches may also be useful for future GWA studies with sequencing data.