3380 Central Expressway
Santa Clara, CA 95051
Phone: 408-731-8000

Brad Margus, CEO
Privately Held


Established in 2000 by Affymetrix Inc., Perlegen Sciences Inc. is a genomics company whose technology centers around Affymetrix’s high-density, whole-wafer microarray technology.

The company’s first objective is to read 50 different human genomes at single base resolution to discover and analyze patterns of genetic variation. Having scanned the genomes, the company will take aim at the entire genomes of specific patient populations provided by pharmaceutical partners seeking to associate genetic patterns with health factors.

Perlegen plans to research the biology underlying genotype-phenotype associations to accelerate the discovery of new drugs and the modification of existing treatments. It also will attempt to develop assays designed to read and determine the genetic profiles of many individuals by reading only a few SNPs from each known block of SNPs.

The company was initiated with $100 million in third-party financing in October 2000. It raised an additional $100 million in private money in April 2001.