August 22, 2005
UCSC researchers awarded grant to develop
faster, cheaper DNA sequencing
By Tim Stephens
A team including researchers at UCSC has received a major grant
from the National Human Genome Research Institute (NHGRI) to
develop new technology for genome sequencing.
The grant is part of an NHGRI program to develop "revolutionary
genome sequencing technologies" that will enable a human-sized
genome to be sequenced for $1,000 or less.
The UCSC researchers are working with collaborators at other
institutions to develop electronic sequencing in nanopores.
David Deamer, research professor of chemistry and biochemistry
and acting chair of biomolecular engineering, and Mark Akeson,
associate adjunct professor of biomolecular engineering, are
pioneers in the development of nanopore technology for DNA analysis.
They will be working with Harvard University researchers Jene
Golovchenko (principal investigator of the project) and Daniel
Branton and University of New Orleans researcher Stephen Winters-Hilt,
who earned his Ph.D. in bioinformatics at UCSC in 2003.
The three-year, $5.2 million grant includes about $1.5 million
for UCSC's part of the project. Deamer said about six researchers
at UCSC will be involved in the effort. The objective of this
project is to develop a general utility instrument to provide
inexpensive sequencing that can also be used for projects to
recognize genome variation. The group will design novel nanopores
articulated with probes to sequentially, and directly, identify
nucleotides in very long fragments of genomic DNA based on their
unique electronic signals.
NHGRI, part of the National Institutes of Health (NIH), announced
the grant August 8 as part of an expanded effort to advance the
development of innovative sequencing technologies by awarding
a dozen new grants totaling more than $32 million. The program
is intended to reduce the cost of DNA sequencing and expand
the use of genomics in biomedical research and health care.
"The efforts are aimed at speeding the rate at which the
next generation of sequencing technologies become available
in the scientific lab and the medical clinic," said NHGRI
director Francis Collins. "Not only will these technologies
substantially reduce the cost of sequencing a genome, but they
will provide a quantum leap in the scope and scale of research
aimed at uncovering the genomic contributions to common diseases,
such as cancer, heart disease, and diabetes."
Over the past decade, DNA sequencing costs have fallen more
than 50-fold, fueled in large part by tools, technologies, and
process improvements developed as part of the successful effort
to sequence the human genome. However, it still costs about
$10 million to sequence 3 billion base pairs--the amount of
DNA found in the genomes of humans and other mammals.
NHGRI's near-term goal is to lower the cost of sequencing a
mammalian-sized genome to $100,000, which would enable researchers
to sequence the genomes of hundreds or even thousands of people
as part of studies to identify genes that contribute to common,
complex diseases. Ultimately, NHGRI's vision is to cut the cost
of whole-genome sequencing to $1,000 or less, which will enable
the sequencing of individual genomes as part of routine medical
care. The ability to sequence an individual genome cost-effectively
could enable health care professionals to tailor diagnosis,
treatment, and prevention to each person's unique genetic profile.
The new grants balance NHGRI's sequencing research portfolio
by supporting more investigators working on technologies that
would make it feasible to sequence a genome for $1,000. The
majority of researchers who received NHGRI's initial sequencing
technology grants, issued in October 2004, are working on technologies
to sequence a genome for $100,000. Both approaches have many
complementary elements that integrate biochemistry, chemistry,
and physics with engineering to enhance the whole effort to
develop the next generation of DNA sequencing and analysis technologies.
"It is very important that we encourage and support the
variety of sequencing technology projects that hold the most
promise for revolutionizing genome sequencing. Each research
team brings a unique set of skills and expertise to solving
difficult scientific and engineering problems," said Jeffery
Schloss, NHGRI's program director for technology development.
"The different approaches will likely yield several successful
and complementary technologies. It is going to be interesting
to see how each technology progresses and which of them can
ultimately be used by the average researcher or physician."
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