Gene and gene-set analysis have been suggested as potentially more powerful alternatives to the typical single-SNP analyses performed in GWAS [7]. In gene analysis, genetic marker data is aggregated to the level of whole genes, testing the joint association of all markers in the gene with the phenotype. Similarly, in gene-set analysis individual genes are aggregated to groups of genes sharing certain biological, functional or other characteristics. Such aggregation has the advantage of considerably reducing the number of tests that need to be performed, and makes it possible to detect effects consisting of multiple weaker associations that would otherwise be missed. Moreover, gene-set analysis can provide insight into the involvement of specific biological pathways or cellular functions in the genetic etiology of a phenotype. Gene-set analysis methods can be subdivided into self-contained and competitive analysis, with the self-contained type testing whether the gene set contains any association at all, and the competitive type testing whether the association in the gene set is greater than in other genes [7].
