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."