The U.S. Department of Commerce has awarded a federal grantworth $31.5 million over five years to Affymetrix Inc., MolecularDynamics, four universities and a non-profit institute to develop ahand-held DNA diagnostic device.The grant, awarded under the Commerce Department's AdvancedTechnology Program, was one of 41 dispensed Monday in fourcategories for a total of approximately $170 million. About $52million were given to companies for development of tools for DNAdiagnostics. All of the grants must be matched with funds from therecipients.The joint venture involving Affymetrix, of Santa Clara, Calif., andMolecular Dynamics, of Sunnyvale, Calif., also includes theLawrence Livermore National Laboratory in Livermore, Calif., theCalifornia Institute of Technology in Pasadena, the University ofCalifornia in Berkeley, the University of Washington in Seattle andStanford University in Palo Alto, Calif.Affymetrix, a subsidiary of Palo Alto-based Affymax, will receive$21.5 million and Molecular Dynamics will get about $10 million.Affymetrix CEO David Singer said with the matching funds theproject is worth about $63 million. "We have some of the matchingfunds and will raise the rest," Singer said.The four universities and Lawrence Livermore, he added, willreceive about $4 million over the five-year life of the joint venture.The objective of the Affymetrix-led project is to develop aminiature integrated nucleic acid diagnostic (MIND). The plan,Singer said, is to integrate in one device the process of takingpatient samples, extracting DNA, amplifying the target DNA andidentifying defects associated with genetic diseases.The project, he added, is in line with Affymetrix's effort to developproducts that will be able to interpret data produced by the HumanGenome Project."There will be so much gene sequencing information out there, thatthe real value will be in understanding the biology so you can moveinto diagnostics and therapeutics," Singer said.Affymetrix's diagnostic device, designed for use in hospitals anddoctors' offices, would be based on its very large scale immobilizedpolymer synthesis (VLSIPS) technology, which involves genesequencing by hybridization.Robert Lipshutz, Affymetrix's director of advanced technology,said VLSIPS is similar to the photolithographic process in thesemiconductor industry."We use light to activate regions on the surface of a DNA chip andinitiate chemical reactions," Lipshutz told BioWorld. "By repeatingthe process over and over we can build up very complex DNAprobes in specific locations on the chip. Then we bring in a sampleof DNA and it reacts with the chip. If it sticks, you have a potentialmatch and by analyzing the hybridization you can detect thesequence of the target DNA."That gets you to genotyping," Lipshutz added. "What we're doingin this project is moving to the next level, preparing targets out ofpatient samples."Affymetrix and Molecular Dynamics, along with the other projectparticipants, will work together in developing the "up-front"technology for incorporating DNA target preparation in thediagnostics. Affymetrix will pursue development of devices basedon VLSIPS while Molecular Dynamics creates tests based on itscapillary array electrophoresis technology for sequencing DNA.The first prototypes of the diagnostic devices will target mutationsin drug-resistant HIV strains. The tests, Affymetrix officials said,could have broad applications in fields such as forensics andagriculture as well as biomedicine.Other companies that received Commerce Department grants in the"tools for DNA diagnostics" category are:- Uniphase Laser Division, San Jose, Calif. ($1.45 million)- GeneTrace Systems Inc., Menlo Park, Calif. ($1.99 million)- Third Wave Technologies Inc., Madison, Wis. ($1.99 million)- Bio-Rad Laboratories, Hercules, Calif. ($2 million)- Hyseq Inc., Sunnyvale, Calif. ($2 million)- Combion Inc., Redwood City, Calif. ($1.79 million)- Vysis, Naperville, Ill. ($2 million)- CuraGen Corp., Bradford, Conn. ($2.27 million)- David Sarnoff Research Center, Princeton, N.J. ($2 million)- Bruker Analytical Systems Inc., Billerica, Mass. ($3.5 million)- E.I. DuPont de Nemours Co., Wilmington, Del. ($2 million)- Molecular Tool Inc., Baltimore. ($1.96 million) n

-- Charles Craig

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