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Arrayit appears in the December 21, 1999 edition of the New York Times.
Biology Meets High Technology; Biochips Signal a Critical Shift for Research and Medicine
By Lawrence M. Fisher
Coming soon, to a chip near you, your own genes.
The biotechnology industry, which has long lived in the shadow of Silicon Valley and envied its many overnight successes, is now tapping into that same technology in a bid to speed up its own growth significantly.
These biochips look like the integrated circuits in a personal computer, but instead of containing tiny semiconductors, they are loaded with bits of actual DNA that make up genes or fragments of genes. Inserted in a PC-sized analytical instrument, the chips allow scientists to perform thousands of biochemical experiments at a fraction of the cost and time required for traditional tests.
''This is a basic tool for change in the laboratory,'' said Michael R. Knapp, vice president for science and technology at Caliper Technologies in Mountain View, Calif. ''We have been operating with the test-tube paradigm for basically as long as anybody has been doing anything.''
Biochips, or microarrays, as they are also known, will bring genomics, the study of all the genes in a living organism, out of the research laboratory and into the daily practice of medicine. If genomics delivers on its promise, health care will shift from a focus on detection and treatment to a process of prediction and prevention. Fortunes will be made.
The initial market for biochips has been in drug discovery, and the major customers have been the large drug companies. By analyzing the subtle changes in genes when a cell becomes cancerous or is infiltrated by a virus, scientists at these companies search for new molecular targets for drugs. This needle-in-a-haystack process could take many years using test tubes and petri dishes but is accelerated a thousandfold by biochip technology.
The market for biochemical research instruments is in the billions, and the transformational power of biochips has not gone unnoticed by the stock market. Shares in Affymetrix, the pioneering company in biochips, have risen more than fivefold the last year, giving the company a market value of about $3.08 billion. Other public companies in the field have had similar gains.
But the biochip makers are now chasing a bigger opportunity: personal genomics. Even as the public and private efforts to spell out the three billion biochemical letters that make up the human genetic code race to a conclusion, the biochip companies say they will bring genomics to an affordable desktop system that could be deployed in clinics and physicians' offices. Sophisticated genetic analysis could be performed at the individual level, making possible early prediction or detection of disease, more accurate diagnosis and customized therapy.
Originally the province of a handful of start-ups backed by venture capital and operating in a sort of gray area between Silicon Valley and the biotech world, the biochip market has lately attracted the attention of major electronics companies like Motorola, Hewlett-Packard, Texas Instruments and I.B.M., all of which have chips in development. Motorola's recent advertisements promote the company's ''digital DNA,'' while those of Hewlett-Packard proclaim the ''DNA of Silicon Valley.'' The message may be metaphoric, but the market is very real.
''The biochip space lies at the intersection between high-technology chip manufacturing, signal processing, software skills and more traditional molecular biology and genomics,'' said Nick Naclerio, vice president and general manager for Motorola's biochip systems division. ''So it seemed right for Motorola to get involved in what we think will ultimately be a big business.''
The biochip companies are one of three new industries that piggybacked on the human genome project, the multinational decade-old effort to identify the 100,000 or more genes -- made from the three billion letters or base pairs of nucleotides -- that inform every aspect of human biology. That project is expected to be completed within a year or two, either by the national labs or private companies or, as seems most likely, a combination of the two.
Genomics companies like Human Genome Sciences, Millennium Pharmaceuticals, Incyte Pharmaceuticals and the Celera Genomics Group of the PE Corporation rushed to beat the public effort by finding and patenting genes of medical utility. Bioinformatics companies, like DoubleTwist.com and Informax, offer software to interpret genomic data. The chip companies, led by Affymetrix, based in Santa Clara, Calif., offer a tool to automate the arduous lab work of biochemical research -- and maybe to do much more.
''We're going to burn a set of chips with the whole human genome,'' said Stephen P. A. Fodor, president and chief executive of Affymetrix. Dr. Fodor headed a group that pioneered the field of biochips, with a 1991 paper in the journal Science describing how photolithography, the standard process by which semiconductor companies etch circuits in silicon, could also be used to synthesize biological materials on a chip.
Companies like Eli Lilly, SmithKline Beecham and American Home Products have been eagerly buying Affymetrix's GeneChip arrays, helping to increase the company's revenues in the first nine months of this year to $65.7 million, from $35.8 million in the comparable period a year earlier.
Often lost in the excitement about the completion of the genome project is that the first human genome will be a consensus, culled from the DNA samples of dozens of anonymous donors. The sequence of each gene will be arrived at only after billions of taxpayer dollars and a decade of study in laboratories lined with $300,000 gene-sequencing machines and other elaborate devices. What the makers of biochips promise is to offer that same depth of information at the individual level and at low cost.
''As soon as the reference DNA is out there, this will move in a thousand different directions,'' Dr. Fodor said.
Nevertheless, most of the chip companies agree that the next big application will be the interpretation of how genetic diversity affects the efficacy and side effects of drugs, a field known as pharmacogenetics. The idea is to use the chips to spot genetic differences known as single nucleotide polymorphisms, or SNP's (pronounced SNIPS), because they consist of a misspelling of just one letter of the genetic code.
A typical person has thousands of SNP's, most of which are inconsequential, but some can predispose one to a disease, or to adverse drug reactions. As researchers discover new SNP's every day, ''SNP's on Chips'' has become a rallying cry for the biochip industry.
''If this SNP enterprise becomes what people think it might, you can imagine having an infant tested at birth and given a chip, and a result that says you are susceptible to diseases A, B and C,'' said Mark Schena, who did early research on biochips while studying at Stanford and is now a visiting scholar at TeleChem International, a biochip company in Sunnyvale, Calif. ''Based on this knowledge you can make appropriate lifestyle changes to prevent the disease or delay its onset''
Such testing, of course, raises many ethical question. Biochip companies are working on encryption technology to keep such data private, but most industry executives believe that legislation will be necessary.
Because the chip companies are all chasing similar markets -- and in part because Affymetrix's early lead allowed it to lock up patents on many of the ways to put DNA on chips -- they are distinguishing their offerings by using different technologies.
Some, like Caliper and Orchid Biocomputer have added microfluidics, a complex network of tiny valves and capillaries that allow researchers to move liquids on and off the chip. Nanogen, based in San Diego, incorporates both microfluidics and electronic circuitry on its chip, to allow researchers to create their own custom microarrays. And Aclara Biosciences of Mountain View, Calif., uses plastic cards instead of glass chips or silicon chips, to keep its devices cheap and disposable.
Orchid, based in Princeton, N.J., has been chosen to perform testing on genetic markers identified by the SNP Consortium, a group of 10 pharmaceuticals companies and 5 academic centers, which expects to find and publish 300,000 SNP's the next two years. Next year, Orchid plans to start GeneShield.com, a Web-based business that will allow consumers to send their own DNA samples, gathered with a simple cheek swab, for analysis against chips loaded with reference SNP's associated with known diseases or drug interactions.
''The number of SNP's being scored now is a horrendous Moore's Law,'' said Dale Pfost, Orchid's president and chief executive, referring to the observation by the Intel co-founder Gordon Moore that the number of devices on a chip would double every 18 months. ''Genetic diversity is a whole new industry that people don't know exists,'' Dr. Pfost said. ''We're enabling that industry.''
As biochips move from the research laboratory to the clinic, the technology must not only achieve something approaching absolute accuracy but also far higher levels of what the industry calls throughput, meaning the number of tests that can be conducted rapidly or simultaneously.
Indeed, evaluating the 300,000 SNP's promised by the consortium in 1,000 people would mean performing 300 million different tests, and any single mistake might create a serious health risk. ''You need an industrial technology for that,'' said Hubert Koster, the chief executive of Sequenom, a San Diego biochip company. ''You cannot use a technology that is 99.9 percent accurate. In the research world that would be O.K., but not in the industrial world because it would give you 300,000 errors.''
The next step will be even more challenging. If biochips are also to aid in quick diagnosis of disease, they need the ability to follow the trail from a gene, which instructs a cell to make a given protein, to the actual proteins produced within the body. Unfortunately, proteins are harder to label and measure then the DNA itself.
''The proteins are the molecular equivalent of a symptom, and your proteins get altered long before you go to a doctor,'' said William Rich, president and chief executive of Ciphergen Biosystems in Palo Alto, Calif., which has developed a protein chip and associated instruments. ''We think the impact on diagnostics will be huge.''
Dr. Schena at TeleChem International agrees. ''Biochips started out with a lot of diagnostics but sort of drifted away from that as reality set in and the pharmaceuticals industry was so needy,'' he said. ''But it will come back. If so, the market is probably in excess of $10 billion a year.''
Some biochip companies are looking well beyond medical applications: genetic diversity also accounts for people's different perceptions of taste and smell. Indeed, Affymetrix already counts a candy manufacturer and a cosmetics company among its customers.
''If you look at a map of the genome, what you see are markers for dysfunction,'' Dr. Fodor said. ''It's a real marketing failure. Let's look at new applications like fragrance or taste. There are going to be a lot of fun things.''
TeleChem International is a privately owned high-tech company located in the heart of California’s Silicon Valley. Our products and services are provided by three corporate divisions: ArrayIt® Life Sciences Division, Chemicals Division, and a Diagnostics Division. The ArrayIt® Life Sciences Division offers a complete microarray technology platform that empowers >10,000 laboratories to use microarrays for human genome exploration, basic research, drug discovery, and myriad life sciences applications. Nearly every major research institution uses our patented microarray manufacturing technology (U.S. 6,101,946) and supporting products and services. The Chemicals Division provides import and export services and government contract manufacturing in the area of industrial chemicals for plastics, fire control, water treatment, agriculture, industrial and institutional compounding, and green energy. The Diagnostics Division holds key patents in the United States (6,913,879), Singapore (94899), New Zealand (523560), and other countries for its revolutionary “multi-patient” genotyping technology, which allows as many as 100,000 patients to be tested on a single microarray. Arrayit Diagnostics enables genotyping and disease diagnostics by providing testing kits, services, and technology transfer opportunities for disease screening and testing organizations.
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