Scientists: Long-promised '$1,000 Gene Sequence' less than two years off
By Lisa M. Krieger


Mercury News

Posted: 06/07/2009 09:21:03 PM PDT
Updated: 06/10/2009 09:52:41 AM PDT


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SETTING THE RECORD STRAIGHT (publ. 6/10/2009)
An article about gene sequencing contained several errors. The leader of the
University of California-San Francisco is chancellor-designate Susan
Desmond-Hellmann. The university's new facility is called the Helen Diller
Family Cancer Research Building. A Mountain View sequencing company is Complete
Genomics, not Complete Genetics.
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They'll be as small as your microwave and cheaper than your laptop. And the
powerful tools — future gene sequencing machines — will be able to tell you
exactly what you're made of. Someday, they could help keep you healthy.

It took 10 years and $4 billion for the federal government to complete the first
sequence of the human genome in 2000. Its equipment filled vast rooms at many
campuses.

Now rival scientific teams, including three in the Bay Area, are racing to build
tests that can accurately sequence an entire human genome in less than 30
minutes for $1,000 — about a hundredth of the current price. The cheaper tests
will make it possible to sequence the genomes of tens of thousands more people,
providing vital data about human traits, such as susceptibility to disease.

Virtuoso bioengineers predict that within two years their tests will start to
transform medicine much as PCs rocked the world of mainframe computing.

Modern genetics is essentially a giant math problem. Which of our 23,000 genes
cause, or protect against, thousands of known illnesses? Do they work alone or
in combinations? How are they affected by the environment?

As more genomes are sequenced, correlations between genes and diseases will
become more apparent.

Currently, scientists searching for rare genetic variants in a population are
rooting for a needle in a haystack, said University of California-San Francisco
Chancellor-Designate Susan Desmond-Hellmann; the university just opened the
Helen Diller Family Cancer Research Building, which will take advantage of the
emerging technology.

As the cost of sequencing drops, and it becomes practical to scan many more
genomes, we'll get much better at "needle-spotting," she said.

Over time, sequencing will move into more diagnostic settings, like community
hospitals. The tests could be used to decipher the genetics not just of healthy
cells, but also out-of-control cancer cells. For instance, there are 38
different genetic subtypes of leukemia. Genomic profiling could help doctors
match the treatment to the precise disease, improving patient outcome and
reducing side effects. That's because some cancer genotypes respond well to
chemotherapy, while others are unaffected.

Mountain View's new Genomic Medicine Institute at El Camino Hospital already
sequences small parts of the genome that are linked to trouble, such as the
breast cancer-related BRCA1 gene, said director Dr. Paul R. Billings.

"Our ability to do it at a better price point means more people will have
access," Billings said. "We will take advantage of continued economies of
sequencing to expand what we offer."

There remain formidable policy problems to solve, such as how to keep such
information private. Also, there is a vast amount of information to be
interpreted and stored.

The acceleration is being propelled by technological innovations. The
performance of gene sequencers has accelerated even faster than that of
microprocessors, which double every 18 months under the famed "Moore's law."
Money is also a motivator. The first team to sequence 100 human genomes in 10
days at a cost of $10,000 or less per genome will be awarded $10 million by the
X Prize Foundation. The market for full-genome sequencing and analysis could be
worth billions.

Rivals include Applied Biosystems of Foster City, as well as Menlo Park's
Pacific Biosystems and Complete Genomics of Mountain View.

The old approach used by the government's Human Genome Project worked by
chopping DNA into short strands, sequencing each strand and then laboriously
stitching them all back together.

Newer generations of the test, such as that offered by the Cambridge,
Mass.-based Knome, are available to private individuals for about $100,000 and
take about two weeks to complete.

"Technologies that are smaller and faster are driving this along," said Mark
Stevenson of Applied Biosystems. In 2010, sequencers will cost about $10,000, he
said.

The price tag will fall to $1,000 by 2011, as technologies like nano-size
chemicals and lasers become more perfected, he predicted.

"The Bay Area plays a critical role, because of our access to leading class
universities and startups," Stevenson said. "The field cuts across fields like
chemistry, biology and IT."

The goal is a full-genome scan, far larger than the tests offered by existing
gene-testing Silicon Valley startups like 23andMe and Navigenics. These
companies test only a tiny part of a person's DNA — certain parts of a
chromosome known as single-nucleotide polymorphisms, or SNPs. Variations in SNPs
are linked to the likelihood of developing certain diseases. But they don't tell
the whole story.

"New technologies are dropping the price and speed," said J. Craig Venter, a
scientific leader in genome sequencing.

"Right now we have a very limited subset of information. Soon we'll have not
just one or 10 genomes — but tens of thousands of genomes."