in turn, can help advance our understanding of the etiology of the trait or disorder. Several different companies now offer GWAS “chips” that have a predefined set of genetic markers that cover genetic variation across the genome. Although the exact markers on the chips vary and companies have used different approaches to select markers, the basic idea is to cover genetic variation across the genome using knowledge about LD patterns (as described above). Through the known LD in the genome, chips with ~1 million markers arrayed on them can track genetic variation down to minor allele frequencies of about 5%, while larger arrays of ~2.5 million markers can track alleles down to about 1% frequency in the population. In this way, there is fairly good coverage of most genes across the genome, as well as intergenic regions (which may contain regulatory elements or have other unknown functions). Another advantage of GWAS is that it provides a built in method to test for genetic background and control for potential population stratification. Population stratification can occur when there are different background allele frequencies and different trait means or prevalences as a function of population membership. In GWAS, having such a large number
