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Perlegen was founded in 2001 as a spin-out from Affymetrix, a genetic tools company. For the first several years of its existence, until about 2004, Perlegen was focused on re-sequencing 50 human genomes, in order to map out the common elements of genetic diversity. During this time, Perlegen developed a majority of the content now publicly available in the "HapMap," or human haplotype map.