Genome-Wide Association Studies provide several advantages over linkage and candidate gene studies. With a sufficiently large sample, it is possible to overcome the lack of power in linkage analyses to detect common alleles with low penetrance. GWAS can also detect much smaller associated DNA regions compared to linkage studies, since linkage analyses are based on rare recombination events in only a few generations, thus resulting in large linked regions. Unlike linkage analyses, GWAS rely on historical recombination events in populations over the course of human history, thus resulting in much smaller regions of association. Furthermore, a great advantage of GWAS over candidate genes studies is the fact that GWAS assume no prior biological knowledge of the disease process, but instead test for association across the whole genome in an agnostic approach. Newer GWAS genotyping platforms now also have the additional benefit of containing copy-number probes to allow examination of both SNPs and CNVs in a single experiment [99, 100].
