Content area
Full Text
Perlegen was founded in late 2000 with the mission of identifying patterns of genetic variation between individuals and using that information to improve patient care and uncover the genetic underpinnings of diseases. With initial funding of US$100 million and technology from Affymetrix, the DNA microchip leader of which Perlegen is an offshoot, the company resequenced over 20 individual human genomes and identified over 1.6 million genetic variations known as single nucleotide polymorphisms (SNPs). This effort was technically possible because of the publicly available first reference sequence created by the Human Genome Project. Perlegen was then able to read multiple whole genomes at a fraction of the cost and time of the original effort and compare them, in order to discover genetic variations that help make each individual human unique.
Perlegen brought unprecedented scale and density to the study of genomics. Allele frequency data for Perlegen's estimated 1.6 million SNPs show that the SNP set is extremely useful for association studies; a large fraction of these SNPs have sizable minor allele frequencies in geographically diverse populations [1]. Perlegen has also identified a subset of approximately 300,000 SNPs, which contain more than 80% of the genetic information of the larger set, suitable for genotyping in individual samples [1,2].
Applying this knowledge, Perlegen quickly developed collaborations with an extensive list of leading research organizations, including six of the world's ten largest pharmaceutical companies, eight separate institutes within the National Institutes of Health (NIH), numerous universities and foundations, and one of the world's larg-est consumer products companies. The company is now conducting comprehensive genetic analyses of several diseases, including: Alzheimer's disease, Parkinson's disease, autism, breast cancer, and metabolic syndrome, in addition to analyzing nicotine addiction. A complete list of Perlegen's publicly announced collaborations is listed on the Perlegen website [101].
In 2004, Perlegen performed over 2 billion genotyping assays, including an unprecedented large-scale genotyping study to estimate the allele frequencies of 1,586,383 SNPs in three diverse populations, generating more than 112 million individual genotypes [1]. Genotypes for over 150,000 of these SNPs had been previously determined by the International HapMap Project, allowing a direct comparison of Perlegen's results with those from HapMap centers. The concordance between Perlegen's genotype data and that obtained from the multiple different platforms used...