Foundation

Perlegen was founded in 2000 within Affymetrix, a genetic tools company, and was spun out and incorporated the following year. 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.

In its early days, Perlegen also worked to establish technology capable of reading DNA faster and less expensively than any then-existing approach. From 2000 to 2003, starting with high-density microarray technology originally developed at Affymetrix, Perlegen’s scientists began working on significantly larger and denser chip formats, combining this massively-parallel technology with novel approaches to DNA sample preparation, optical scanning and computational analysis. The result was a system that could read single nucleotide polymorphism (SNP) genotypes in DNA over 100 times faster and cheaper than the capillary-gel electrophoresis technology used by the Human Genome Project to sequence the first copy of the human genome.

Expansion and Application

From this foundation, Perlegen worked on several dozen projects with a variety of pharmaceutical companies, academic institutions and research organizations to understand the way that these common elements of genetic diversity interacted with predisposition to disease and variable response to treatment.

During this period, from 2004 to 2006, Perlegen began to understand the importance of individually rare, as well as widespread, elements of genetic variability in understanding individual responses to disease and treatment. These insights led the way to Perlegen’s current capabilities in sequencing and to our emphasis on carefully selected clinical issues and tailored sample collection capabilities.

Commercialization

Perlegen now is working to bring its discoveries to market, using next-generation sequencing technology to catalog nearly all genetic variations—not just SNP genotypes—associated with a particular clinical situation. Perlegen is set to deliver an entirely new category of genetic discoveries by finding the networks of genetic control indicated by more rare variants with larger effects.