Affymetrix spins off genomics company
New company will sequence 50 individuals in its first year
Affymetrix Inc. (Santa Clara, CA) has formed a new genomics subsidiary called Perlegen Sciences Inc. With approximately $100 million in third party financing, the new company will use Affymetrix' latest DNA scanning technology to read 50 human genomes and identify the millions of genetic variations between individuals and look for patterns in those variations. It will then work with pharmaceutical partners to associate the patterns with health factors and drug responses.
Perlegen, which derives its name from the Latin word "perlego"—which means "to scan, to survey thoroughly, or to read through—will be recruiting additional scientists, scaling up biological sample processing, and building a massive database system to become a source of information about patterns of genetic variation between individuals and how those patterns are associated with health and disease. Once it has scanned 50 genomes, the company will use these technologies and the patterns to scan entire genomes of specific patient populations provided by pharmaceutical partners.
Brad Margus, who was recruited earlier this year to head the genome scanning project at Affymetrix, will be the CEO of Perlegen Sciences. Margus has been a national advocate for biological research on behalf of people impacted by genetic disorders. He believes that the new company's approach will have significant commercial and societal value.
"This new biotech firm will be first in showing that genome-wide genetic differences play an important role in how the body reacts to the environment, develops disease or responds to drugs. We hope to demonstrate an entirely new paradigm of whole genome patterning," noted Margus. "Scientists will be able to understand how an individual's many genes interact with each other, greatly accelerating the drug development process and increasing the research productivity of drug companies."
Perlegen will have exclusive access to whole wafer technology developed by Affymetrix. The genome scanning technology now being used includes novel substrate chemistry, wafer synthesis, sample preparation, and innovative scanning techniques that allow for the production of DNA arrays that place over 60 million DNA probes on a single glass substrate. Perlegen Sciences will become a major customer of Affymetrix, which will retain a substantial equity position in Perlegen.
In conjunction with high resolution scanning technology available to read each DNA sample, Perlegen Sciences will also be using a somatic cell genetic approach to separate each pair of a person's chromosomes before reading the individual's genetic profile. In taking this extra step, which involves fusing human cell lines with rodent cells, Perlegen Sciences will be able to detect genetic variations in each chromosome separately.
"By identifying millions of biologically significant variations between individuals and associating genome-wide patterns with clinical findings, we'll help researchers around the world narrow their searches for genes that affect the management of health," said David R. Cox, who will be scientific director for the new company. Cox, professor of pediatrics and genetics at the Stanford University School of Medicine and co-director of Stanford's Genome Center, took a sabbatical from Stanford earlier this year in order to lead the scientific effort at Affymetrix to scan entire genomes. "I wanted to be part of this ambitious plan to compare the entire DNA profile of numerous individuals for the first time in history," Cox explained.
Stephen Fodor, chairman and CEO of Affymetrix, believes that comparing the genetic profiles of numerous individuals will create enormous value. "So far, no one has had adequate technology to look at whole genome patterns found across many individuals," said Fodor, who will serve as the new firm's chairman. "It's thrilling to see the power of Affymetrix' technology once again being exploited for new opportunities."
Perlegen's Scientific Advisory Board include Nobel Laureate Paul Berg, director of the Beckman Center for Molecular and Genetic Medicine at Stanford University; Aravinda Chakravarti, director of the Johns Hopkins School of Medicine's McKusick-Nathans Institute for Genetic Medicine; Jasper Rine, professor of genetics at the University of California, Berkeley; Edward Rubin, head of Genome Sciences at Lawrence Berkeley National Laboratory; and Lubert Stryer, professor of neurobiology at Stanford.
Specific details of the agreements between Perlegen Sciences and Affymetrix were not disclosed, and the agreements are subject to final documentation and the approval of the Board of Affymetrix.
For more information: Affymetrix Inc., 3380 Central Expressway, Santa Clara, CA 95051. Tel: 408-731-5000. Fax: 408-481-0422.
Edited by Laura DeFrancesco
Managing Editor, Bioresearch Online
ldefrancesco@bioresearchonline.com
Souce: Affymetrix