epistasis

Moore JH, Asselbergs FW & Williams SM 2010 Bioinformatics challenges for genome-wide association studies. Bioinformatics 26:445-455.

• most SNPs discovered via GWAS have small effects on disease susceptibility and thus may not be suitable for improving health care through genetic testing
• the linear modeling framework that is employed in GWAS often considers only one SNP at a time thus ignoring their genomic and environmental context

• Askland et al. (2009) recently showed that patterns of SNPs in biological pathways are more likely to replicate than individual SNPs in GWAS
• this is highly consistent with the idea that interactions may be more important that [than?] marginal effects
• Wilke et al. (2008) have suggested that we should not even begin to analyze a GWAS until we have exhaustively studied each candidate gene and each pathway