Gene Sequencing for the Masses
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Kristina Kirby
Apr 30, 2008, 12:22:59 PM4/30/08
to EmergingTechnologies
Wednesday, April 30, 2008
Technology Review
Gene Sequencing for the Masses
A genomics pioneer's sequencing machine comes to market.
By Emily Singer
http://www.technologyreview.com/Biotech/20696/?nlid=1038
***********************************************
An inexpensive new gene-sequencing machine is due to hit the market
next month, and its creators hope that it will make sequencing more
common, ultimately giving a boost to personalized medicine. The
machine is the brainchild of George Church, a genomics pioneer who
developed the first direct sequencing technology as a graduate student
in the 1980s and helped initiate the Human Genome Project soon after.
Church sees greater access to sequencing as a vital component in the
drive toward personalized medicine, in which treatments and
preventative medicine are tailored to an individual's genetic makeup.
The new machine, which was developed with an "open source" philosophy,
was commercialized by Danaher Motion, based in Salem, NH, with the
specific intent of keeping costs low. "It seems like the biomedical-
instrument field in general tries not to commoditize," says Church,
who heads the Center for Computational Genetics at Harvard Medical
School, in Boston. "It tries to keep profit margins high and slow the
inevitable decrease in cost." The Danaher device will cost roughly
$150,000, a third to a tenth of the cost of systems currently on the
market.
The technology will become an integral part of Church's other
brainchild, the Personal Genome Project, an effort to enable
personalized medicine by providing a test bed for new genomics
technologies and analytic tools. Church and his collaborators are
using the new device to sequence the genomes of the project's first 10
volunteers, who will share their genome sequences, medical records,
and other personal information with both scientists and the public.
Church hopes that, ultimately, thousands of people or more will have
their genomes sequenced as part of the project, and that the result
will be a huge compendium of data that is useful to both the
volunteers themselves and to the research community. "Part of the goal
of this project is as a bridge between the research market, which is
small, and the consumer market," says Church.
Church's group has spent the past several years developing prototypes
of the sequencing device--known as the Polonator--from off-the-shelf
components. Church originally planned to create an instruction manual
for building a Polonator from scratch and post it on the Internet, but
he ultimately decided that it would be more effective to develop a
commercial device. His team partnered with Danaher Motion, a precision-
instrument maker that built movable microscope stages for earlier
versions of the technology. Over the past year, Danaher has worked
with Church to develop the cheapest and most robust system possible.
"I could sell them at $300,000, but George has a mission of sequencing
for the masses," says Kevin McCarthy, chief technology officer at
Danaher. "At $150,000, I can still provide profit margins for our
shareholders and make George happy."
The device is a commercial version of the polony sequencing approach
developed in Church's lab over the past 10 years. Millions of beads
coated with small fragments of the DNA to be sequenced are spread on a
glass slide. Next, a series of fluorescently labeled DNA bases bind to
the fragments. Finally, a standard fluorescence microscope reveals
which base is at each position on a fragment. (The commercial version
of the technology can accommodate a billion beads and has a more
sophisticated imaging instrument.)
While the scientists don't yet have the final figures on the
Polonator's accuracy and throughput, they expect that it will sequence
10 billion base pairs in a single 80-hour run, a capacity equal to or
greater than that of currently available technologies. Harvard and
MIT's jointly run Broad Institute for genomic medicine, in Cambridge,
MA, and the Max Planck Institute, in Germany, have already purchased
devices at the $150,000 sticker price, and the machines should be
delivered within the next week or two. General availability is
expected by mid- to late May.
Despite almost no marketing, the Polonator has already created a buzz
in the research community. McCarthy brought a prototype to a
sequencing conference in Florida earlier this year and says that
people were lined up to see it until the early hours of the morning.
Last week, scientists at a genome-sequencing conference in San Diego,
where McCarthy gave his first public presentation on the technology,
found the concept intriguing. One of those in attendance was Vladimir
Benes, head of the genomics core facility at the European Molecular
Biology Laboratory, in Heidelberg, Germany. "It's definitely in the
spirit of George Church to make technology as accessible as possible
and let the community do what they like," Benes said at the time.
Patrice Milos, chief scientific officer at Helicos BioSciences, a
company based in Cambridge, MA, that has just released its own
sequencing machine, had a more muted reaction. "As with any
technology, it's seeing what they can deliver that matters," Milos
said.
The Polonator embodies an open-source philosophy. It was designed so
that users can tinker with it in any way they wish. All the parts can
be swapped out, and scientists can use enzymes and chemicals other
than those sold by Danaher for the sequencing process. Church and
others are already working on alternative chemical processes that
could make the instrument more efficient. "The fact that it's open
source is great," says Andrew Barry, supervisor of process development
at the Broad Institute. "It's going to be a community-driven
instrument."
Church believes that sequencing will ultimately be a more effective
personalized-medicine tool than the microarray technologies currently
on the market. (Several companies now offer chips studded with small
pieces of DNA that can be used to detect specific genetic variations
linked to disease.) By looking at the entire genome, sequencing is
able to identify mutations that microarrays cannot. "Sequencing is
turning out to be as cost effective at most things as chips are now,"
Church says. "And you can do things with sequencing you can't do with
chips."
**************************************
Copyright Technology Review 2008.
http://www.technologyreview.com/Biotech/20696/?nlid=1038
Technology Review
Gene Sequencing for the Masses
A genomics pioneer's sequencing machine comes to market.
By Emily Singer
http://www.technologyreview.com/Biotech/20696/?nlid=1038
***********************************************
An inexpensive new gene-sequencing machine is due to hit the market
next month, and its creators hope that it will make sequencing more
common, ultimately giving a boost to personalized medicine. The
machine is the brainchild of George Church, a genomics pioneer who
developed the first direct sequencing technology as a graduate student
in the 1980s and helped initiate the Human Genome Project soon after.
Church sees greater access to sequencing as a vital component in the
drive toward personalized medicine, in which treatments and
preventative medicine are tailored to an individual's genetic makeup.
The new machine, which was developed with an "open source" philosophy,
was commercialized by Danaher Motion, based in Salem, NH, with the
specific intent of keeping costs low. "It seems like the biomedical-
instrument field in general tries not to commoditize," says Church,
who heads the Center for Computational Genetics at Harvard Medical
School, in Boston. "It tries to keep profit margins high and slow the
inevitable decrease in cost." The Danaher device will cost roughly
$150,000, a third to a tenth of the cost of systems currently on the
market.
The technology will become an integral part of Church's other
brainchild, the Personal Genome Project, an effort to enable
personalized medicine by providing a test bed for new genomics
technologies and analytic tools. Church and his collaborators are
using the new device to sequence the genomes of the project's first 10
volunteers, who will share their genome sequences, medical records,
and other personal information with both scientists and the public.
Church hopes that, ultimately, thousands of people or more will have
their genomes sequenced as part of the project, and that the result
will be a huge compendium of data that is useful to both the
volunteers themselves and to the research community. "Part of the goal
of this project is as a bridge between the research market, which is
small, and the consumer market," says Church.
Church's group has spent the past several years developing prototypes
of the sequencing device--known as the Polonator--from off-the-shelf
components. Church originally planned to create an instruction manual
for building a Polonator from scratch and post it on the Internet, but
he ultimately decided that it would be more effective to develop a
commercial device. His team partnered with Danaher Motion, a precision-
instrument maker that built movable microscope stages for earlier
versions of the technology. Over the past year, Danaher has worked
with Church to develop the cheapest and most robust system possible.
"I could sell them at $300,000, but George has a mission of sequencing
for the masses," says Kevin McCarthy, chief technology officer at
Danaher. "At $150,000, I can still provide profit margins for our
shareholders and make George happy."
The device is a commercial version of the polony sequencing approach
developed in Church's lab over the past 10 years. Millions of beads
coated with small fragments of the DNA to be sequenced are spread on a
glass slide. Next, a series of fluorescently labeled DNA bases bind to
the fragments. Finally, a standard fluorescence microscope reveals
which base is at each position on a fragment. (The commercial version
of the technology can accommodate a billion beads and has a more
sophisticated imaging instrument.)
While the scientists don't yet have the final figures on the
Polonator's accuracy and throughput, they expect that it will sequence
10 billion base pairs in a single 80-hour run, a capacity equal to or
greater than that of currently available technologies. Harvard and
MIT's jointly run Broad Institute for genomic medicine, in Cambridge,
MA, and the Max Planck Institute, in Germany, have already purchased
devices at the $150,000 sticker price, and the machines should be
delivered within the next week or two. General availability is
expected by mid- to late May.
Despite almost no marketing, the Polonator has already created a buzz
in the research community. McCarthy brought a prototype to a
sequencing conference in Florida earlier this year and says that
people were lined up to see it until the early hours of the morning.
Last week, scientists at a genome-sequencing conference in San Diego,
where McCarthy gave his first public presentation on the technology,
found the concept intriguing. One of those in attendance was Vladimir
Benes, head of the genomics core facility at the European Molecular
Biology Laboratory, in Heidelberg, Germany. "It's definitely in the
spirit of George Church to make technology as accessible as possible
and let the community do what they like," Benes said at the time.
Patrice Milos, chief scientific officer at Helicos BioSciences, a
company based in Cambridge, MA, that has just released its own
sequencing machine, had a more muted reaction. "As with any
technology, it's seeing what they can deliver that matters," Milos
said.
The Polonator embodies an open-source philosophy. It was designed so
that users can tinker with it in any way they wish. All the parts can
be swapped out, and scientists can use enzymes and chemicals other
than those sold by Danaher for the sequencing process. Church and
others are already working on alternative chemical processes that
could make the instrument more efficient. "The fact that it's open
source is great," says Andrew Barry, supervisor of process development
at the Broad Institute. "It's going to be a community-driven
instrument."
Church believes that sequencing will ultimately be a more effective
personalized-medicine tool than the microarray technologies currently
on the market. (Several companies now offer chips studded with small
pieces of DNA that can be used to detect specific genetic variations
linked to disease.) By looking at the entire genome, sequencing is
able to identify mutations that microarrays cannot. "Sequencing is
turning out to be as cost effective at most things as chips are now,"
Church says. "And you can do things with sequencing you can't do with
chips."
**************************************
Copyright Technology Review 2008.
http://www.technologyreview.com/Biotech/20696/?nlid=1038
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