In the effort to discover novel variants, we believe strongly that traditional candidate gene studies are to be discouraged in favor of GWAS. Genome-wide arrays are cheap, with suitable arrays selling for less than $50 per DNA sample including DNA preparation costs. Genome-wide arrays can be used effectively with DNA extracted from saliva or blood. They provide coverage of the entire genome, often with custom content including additional coverage of small gene sets. GWAS arrays leverage the fact that genetic variants are not independent. Recombination during meiosis creates segments of DNA that are inherited as a unit, creating a correlation among the base pairs within it, a phenomenon known as “linkage disequilibrium” or LD. Present day arrays use SNPs that are selected to carefully tag the LD structure of the genome, effectively allowing one to test the vast majority of common genetic variants in the human genome. Even better, genotype imputation works well with these SNPs to provide extremely dense and accurate measurements of nearly all common SNPs in the human genome. This increases statistical power for any particular variant
