At present, high-throughput genome-wide association study (GWAS) methods are the most common hypothesis-free approach to genetic association. Like linkage, GWAS provides systematic coverage of the genome, without a priori hypotheses about where causal variants are likely to be located. The basic question in an association study is whether individual differences in a phenotype correspond to allele differences in a SNP. In a GWAS, hundreds of thousands to millions of SNPs are tested for association in this way. To date, gene identification efforts for complex traits have been notoriously difficult, and it is becoming increasingly clear that large sample sizes are required.
