Cool; I get to respond to myself. There is something Goedel-Escher-Bach in this. So here's the dope on the amazing GeneChip, very Jurassic Park:
(From Wired Magazine, "Hacking the Mother Code"):
So how does this work, anyway?
To better diagram the complicated elegance of Affymetrix's invention,
Fodor leaves the limitations of felt pen and white board behind. He
moves to a dimmed conference room where a series of color slides
softly click one after another, revealing the innards of the GeneChip.
A small wafer of silica provides the ideal base for the GeneChip.
Extremely expensive refined glass, silica is both optically transparent (meaning genetic results can be scanned by an optical reader) and capable of supporting the chemical reactions that anchor DNA to the chip.
To make a GeneChip, the silica wafer is first primed to accept genetic
material, then alternately washed with a solution of synthetic nucleotides (the building blocks of DNA) and exposed to intense light in rigidly defined surface areas. This creates "stacks" of synthetic, genetic code which, under a microscope, appear to jut up from the wafer like an eerie, microscopic skyline of three-dimensional genetic "buildings" of information. However, these structures contain only half the DNA code. The other half of the code, the half that will provide an answer to the medical question at hand, resides in the patient's blood.
The DNA double helix is an elegant "zipper" built of nucleotides that
join together in strict sequence: guanine (G) can bind only to cytosine (C); adenine (A) can bind only to thymine (T). The two halves of the helix are therefore rigidly complementary. Affymetrix's GeneChip metaphorically acts as one half of the zipper, say the gene for Huntington's disease, while a specially treated sample of DNA from the patient's blood acts as the other, complementary half.
Should a patient want to know whether he or she is a carrier for
Huntington's, an amplified sample of blood is flowed over the chip.
The DNA in that sample adheres only to its complementary counterparts - those rectangular "buildings" of DNA. The chip is then scanned by a laser reader resembling nothing so much as a minute record-player arm. This reveals genetic sequence matches. The locations of these points of contact are then read and analyzed in software. In a matter of half an hour, the doctor and patient have their answer, and it all costs less than your average ATM withdrawal.
The Intel of biochips?
Affymetrix will stand its ultimate test in the biotech market. It's no secret that the biotech boom has left a moraine of false promises and failed products in its wake. Many one-product start-ups face heightened skepticism about hype and vaporware. Affymetrix is no exception. John Patton, a scientist formerly with Genentech, now vice president of research for Inhale Therapeutic Systems in Palo Alto, is a veteran of the industry. By no means dismissive of Affymetrix's claims, Patton has nevertheless "become sober about company executives touting sexy new biostuff. Unless Affymetrix can show some patient results, it's still just an idea, and may not work at all."
But the potential commercial market is huge. "In five years, we'll know technically if we can compress the front-end biology stuff, miniaturizing the lab steps into an automated, hand-held device," says Dave Singer, vice chair of Affymetrix. "In 10 years, we'll see the impact of the basic, non-automated GeneChip on the market." The potential profits that could be generated by this Intel of the biochip world makes Affymetrix, Singer claims, "hellbent on getting this technology to market ASAP."
And with good reason. "In the pharmaceutical industry, being the first
to market usually allows you to control about 30 percent of it," explains Schaefer Price, an industry analyst and vice president of Burrill & Craves. "However, there are huge risks involved in being thefirst. You must be the first to tackle regulatory issues and governing bodies. You must educate them about your product. This takes a great deal of time and expense."
The first specialized product Affymetrix hopes to roll out will be the
GeneChip HIV system, a chip promising doctors the ability to prescribe related drugs more effectually. Various cancer arrays and other chip collections will follow.
Once the process is fully automated, mass production of the disposable
GeneChip will offer a hostof applications in the private sector, while
bringing the cost ofgenetic screening down. "The chip industry, which
is now about 30 years old," says Singer, "has transformed the global
economy. We're hoping that 30 years from now, our chips will have done the same thing for genetics."
(From Affymetrix' webpage):
Affymetrix
3380 Central Expressway , Santa Clara,California 95051 U.S.A.
Phone: 408-552-6033 Fax: 408-481-0920 E-mail: n/a
Key Statistics
Industry: Biotechnology
Segment: Human Diagnostics
Ownership: Private (Not anymore! FQ)
Employees: 89
Collaborations: none
Revenue: n/a (US $ mil.)
Profile
Affymetrix is developing and commercializing GeneChipTM systems to acquire, analyze, manage and use genetic information based on its proprietary DNA array technology. These systems are being developed for broad fields including biomedical research, clinical diagnosis and the emerging field of genomics. Affymetrix has corporate alliances with the Hewlett-Packard Company and Genetics Institute. Affymetrix intends to pursue the clinical diagnostic and additional genomics applications with established diagnostic and pharmaceutical companies, respectively. Glaxo Wellcome plc (NYSE: GLX) owns 47% of the equity of Affymetrix. Located in Santa Clara, California, Affymetrix has 89 employees.
The company's first product, which is currently in external test sites, will be the GeneChip HIV system which rapidly detects mutations in the protease and reverse transcriptase genes of HIV, the virus which causes AIDS. Detection of such mutations are critical in understanding how HIV reacts to therapeutic agents and for understanding the results of clinical trials of new drugs. The company also has active development programs for the speciation of other infectious organisms as well as for human genes that are important in cancer and drug metabolism.
Elaine Heron, Ph.D.
Vice President, Marketing
Hope you find it interesting.
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