Is there still a need for candidate gene approaches in the era of genome-wide association studies?

Most genetic variants associated with complex diseases in humans are believed to have a small impact on risk. With traditional candidate gene/pathway approaches several associations with disease risk could be identified. However, now that genome-wide association studies are feasible, the question arises if there is still a need for these approaches. By using HapMap data, we evaluated to which extent commercially available microarrays cover, through linkage disequilibrium, all currently known genes and biological processes in different populations. Furthermore, we estimated the power to detect an association with any specific SNP. Our study shows that coverage of individual genes and pathways by current commercial genotyping platforms is satisfactory for the vast majority of RefSeq gene regions. However, depending on the gene or the population, there may still be a need for candidate gene approaches, especially when looking at polymorphisms with low allele frequencies.