Genome-wide association studies were made possible by the availability of chip-based microarray technology for assaying one million or more SNPs. Two primary platforms have been used for most GWAS. These include products from Illumina (San Diego, CA) and Affymetrix (Santa Clara, CA). These two competing technologies have been recently reviewed [20] and offer different approaches to measure SNP variation. For example, the Affymetrix platform prints short DNA sequences as a spot on the chip that recognizes a specific SNP allele. Alleles (i.e. nucleotides) are detected by differential hybridization of the sample DNA. Illumina on the other hand uses a bead-based technology with slightly longer DNA sequences to detect alleles. The Illumina chips are more expensive to make but provide better specificity.
