A race to market the whole-genome chip
 
Andrew Pollack NYT
Friday, October 3, 2003
The genome on a chip has arrived. Melding high technology with biology, several companies are rushing to sell slivers of glass or nylon, some as small as postage stamps, packed with pieces of all 30,000 or so known human genes.
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The new products will allow scientists to scan all genes in a human tissue sample at once to determine which are active, a job that previously required two or more chips. The whole-genome chips will lower the cost and increase the speed of a widely used test that has transformed biomedical research in the last few years.
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"It's sort of a milestone event, very similar to generating an integrated circuit of the genome," said Stephen Fodor, chief executive of Affymetrix, the leading seller of gene chips, which are also called microarrays.
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Affymetrix, based in Santa Clara, California, announced on Thursday that it was accepting orders for its whole-genome chip.
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The announcement seemed timed to steal some thunder from the rival Agilent Technologies, based in nearby Palo Alto, which announced Thursday that it had started shipping test versions of its own whole-genome chip.
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Applied Biosystems of Foster City, California, a unit of Applera, started the race in July with an announcement that it would have a whole-genome chip out by the end of this year. NimbleGen Systems, a small company in Madison, Wisconsin, announced a few days later that it had a genome on a chip that it was not selling but that it was using to run tests for customers.
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Gene chips, which detect genes that are active, meaning they are being used to make a protein, have become essential tools. Scientists try to understand the genetic mechanisms of disease by seeing which genes are turned on in, say, a sick kidney or lung compared with those active in a healthy organ. Pharmaceutical companies look at gene activity patterns to try to predict the effects of drugs. Scientists have found that tumors that look the same under the microscope can differ in gene activity. So studying gene patterns could become a way to discriminate between deadly and not-so-deadly tumors, or to determine which drug will work best for a particular patient. Still, even some vendors conceded that the change from two chips to one is more symbolic than revolutionary. "You can do just as good science with two chips - it costs you a little more," said Roland Green, the vice president for research and development at NimbleGen.
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The advent of the genome on a chip is evidence that biotechnology, to the extent that it uses electronics, is experiencing some of the same rapid progress that has made semiconductors and computers cheaper and smaller.
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"One of the effects everyone is looking for in the genomics area is Moore's law - more data, less money," said Doug Dolginow, an executive vice president at Gene Logic, which sells data from gene chip studies to pharmaceutical companies. "This is a step in that direction." Moore's law states that the number of transistors on a semiconductor chip doubles every 18 months.
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Affymetrix's gene chips are, in fact, made with the same techniques used to make semiconductor chips. In the mid-1990's, the company came out with a set of five chips covering what was then known of the human genome. After the human genome sequence was virtually completed in 2000, it developed a two-chip set with all the known genes. Now it has the single chip, which some scientists say will be more convenient.
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"We like to be able to look at all genes at one time to get a global view of what's going on," said John Walker, who runs gene chip operations at the Genomics Institute of the Novartis Research Foundation in San Diego.
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Affymetrix said it would sell its whole-genome chips for $300 to $500 each, depending on volume, little more than half the price of the two-chip set.
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The New York Times

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