X-Message-Number: 15313
From: "Mark Plus" <>
Subject: "Biochips" article on Reason.com
Date: Wed, 10 Jan 2001 14:09:24 -0800

From:

http://reason.com/rb/rb011001.html

January 10, 2001

Biochips Ahoy!

By Ronald Bailey, Reason Science Correspondent

"This is the year we re going to see improvements in health care as a result 
of Affymetrix chips," declared Mark Hurt, a senior field applications 
specialist for the biotech company, at a recent seminar at the University of 
Virginia Medical Center. The seminar was so popular that it had to be moved 
to a much larger auditorium -- and even then, some of the overflow audience 
of doctors, researchers and med students had to sit in the aisles. The 
excitement was over the research and medical treatment possibilities offered 
by Affymetrix s biochips.

Founded in the early 1990s, California-based Affymetrix has developed system 
for quickly analyzing the genetic codes of human beings and many other model 
organisms, including mice, fruit flies, and yeast. Affymetrix's technique 
combines the photolithography of semiconductor manufacturers with 
biochemistry to create gene chips. Each gene chip consists of an array of 
tiny wells measuring 20 microns square on a 1.3 centimeter silicon chip. In 
each well are DNA probes that can detect the presence of a specific gene. 
Because the chips are created using up to 75 different layers, the 
"complexity of making a gene chip is equal to that used in the semiconductor 
industry," said Hurt. Affymetrix no longer has the biochip field to itself. 
Corning, for example, has worked out a deal to develop biochips with the 
Whitehead Institute in Cambridge, Massachusetts, one of the leading public 
human genome sequencing centers.

Biochips will be an essential technology for deciphering the human genome, 
i.e., the entire genetic sequence of all human DNA soon to be published by 
scientists at Celera Genomics and the international Human Genome 
Organization. The human genome is a string of some 3 billion As, Cs, Gs and 
Ts, the chemical building blocks of the genetic code. This sequence is being 
made available to researchers through both public and private databases. 
Determining what the sequences mean for human health and development will 
likely take decades to puzzle out.

What role will biochips play? Right now biochips are being used by 
researchers to find out which genes are expressed in which tissues. Nearly 
every human cell contains the entire genome, but to create the various 
tissues that make up the human body, different genes have to be turned on or 
off. In any given cell -- a liver cell, say, or a skin cell -- perhaps only 
15 percent of its genes are active. Biochips can tell researchers what those 
genes are. They can find out the differences between healthy and diseased 
tissues and thus suggest different therapeutic targets. For example, 
Affymetrix has a chip that can be used to distinguished between cancers 
based on whether the p53 tumor-suppressor gene has been inactivated or not. 
This is important because more aggressive treatment regimens are called for 
if the p53 gene is not functioning. At the UVA seminar, Dr. Meng Chen 
described how her lab used biochips to determine which genes the new drug 
lisofylline turns off and on. That knowledge will enable researchers to 
figure out how to protect insulin-protecting pancreatic cells from damage 
that could lead to diabetes.

Currently, Affymetrix has a biochip that can detect the presence of 12,500 
different human genes. "It is our goal as a company to bring you the entire 
human genome on a single chip array," Hurt told the audience. "Probably not 
in 2001, but maybe next year." Affymetrix is also working with the 
pharmaceutical giant Glaxo Wellcome to create a biochip that will 
distinguish between 100,000 different single-nucleotide polymorphisms, 
(SNPs, pronounced "snips"). SNPs are what account for human genetic 
variation ranging from hair and eye color to propensities to diabetes and 
heart disease. Ten leading pharmaceutical and information technology 
companies donated $50 million dollars to the public genome project to create 
the SNPs Consortium. So far 2.5 million SNPs have been discovered. Francis 
Collins, Director of the National Human Genome Research Institute estimates 
that out of some 10 million SNPs, about 200,000 will turn out to be 
functionally important.

Biochips will enable researchers to compare whole constellations of SNPs 
between people to discover how this or that genetic variation correlates 
with this or that disease outcome. For example one constellation of SNPs 
might dispose those who have it to early-onset dementia, while another SNPs 
pattern might indicate a higher risk of kidney failure. Every human being 
probably has 40 to 50 genetic "glitches" predisposing them to various 
diseases, according to Collins.

Pharmaceutical companies are betting that SNPs will hold the key to 
explaining why specific drugs cause severe side effects in some people while 
offering tremendous benefits to others. If researchers can distinguish 
between those patients a medicine will harm vs. those it will help, many 
therapies that are currently shelved because their side effects cannot be 
predicted in specific patients could be brought safely to market. SNPs 
research also raises socially and ethically problematic issues, such as 
uncovering possible genetic correlations for alcoholism, violence, and 
intelligence.

Biochips are not cheap, though the price is falling rapidly. A year ago, 
human biochips cost $2,000 per unit. Currently human biochips cost $1,000, 
while chips for mice, yeast, and fruit flies cost around $400 to $500. The 
price for human biochips will probably drop to $500 this year. Once all the 
human genes are well characterized and all functional human SNPs are known, 
manufacture of the chips could conceivably be standardized. Then, prices for 
biochips, like the prices for computer memory chips, would fall through the 
floor.

Your doctor might one day routinely put a bit of your DNA on a biochip and 
pop it into an office scanner to perform a full genetic scan as part of your 
regular physical. Or she might use biochips designed to detect disease 
organisms to precisely diagnose which kind of germ is causing your stomach 
flu. Biochips could thus finally usher in the era of medicine tailored to 
each individual patient.

Ronald Bailey () is Reason Magazine's science 
correspondent.



_________________________________________________________________
Get your FREE download of MSN Explorer at http://explorer.msn.com

Rate This Message: http://www.cryonet.org/cgi-bin/rate.cgi?msg=15313