NHGRI Seeks DNA Sequencing Technologies Fit for Routine Laboratory and Medical Use
The National Human Genome Research Institute (NHGRI), part of
the National Institutes of Health (NIH), today awarded more than
$20 million in grants to develop innovative sequencing technologies
inexpensive and efficient enough to sequence a person’s DNA as
a routine part of biomedical research and health care.
"The ability to sequence any individual’s genome inexpensively and accurately is the quantum leap needed to usher in an age of personalized medicine, in which healthcare providers will routinely use an individual’s genetic code to prevent, diagnose, and treat diseases"said Alan E. Guttmacher, M.D., acting director of the National Human Genome Research Institute.
DNA sequencing costs have fallen dramatically over the past decade, fueled in large part by tools, technologies and process improvements developed as part of the successful effort to sequence the human genome. NHGRI subsequently launched programs in 2004 to accelerate the development of sequencing technologies and the rate of reduction of genome sequencing cost. Significant progress has been made towards the goal of producing high quality genome sequence of 3 billion base pairs — the amount of DNA found in humans and other mammals – for $100,000. Ultimately, NHGRI’s vision is to cut the cost of whole-genome sequencing of an individual’s genome to $1,000 or less, which will enable sequencing as part of routine medical care.
"A new generation of sequencing technologies is stepping in front of the already impressive technologies that enabled initial sequencing of the human genome," said Jeffery Schloss, Ph.D., NHGRI's program director for technology development. "We continue to seek further innovation to enable routine sequencing of genomes to advance scientific knowledge and healthcare."
The new grants will fund eight investigator teams to develop revolutionary technologies that would make it possible to sequence a genome for $1,000, as well as three investigators developing nearer-term technologies to sequence a genome for $100,000. The collective approaches incorporate 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.
"$1,000 Genome" Grants
NHGRI’s Revolutionary Genome Sequencing Technologies grants have as their goal the development of breakthrough technologies that will enable a human-sized genome to be sequenced for $1,000 or less. Grant recipients and their approximate total funding are:
Daniel Branton, Ph.D., Jene A. Golovchenko, Ph.D., Harvard University, Cambridge,
$6.5 million (4 years)
Electronic Sequencing in Nanopores
Several groups are developing nanopores (holes about two nanometers in diameter) that may be able to recognize individual DNA bases by their electrical or ionic signals to achieve high-accuracy sequencing of individual DNA molecules. The goal of this group is to design and optimize nanopore technology using novel electronic control and sensing methods to eventually lead to a nanopore detector chip capable of sequencing a mammalian genome within a day on a single instrument.
Stephen Y. Chou, Ph.D., Princeton University, Princeton, New Jersey
$920,000 (3 years)
Nanogap Detector (Arrays) Inside Nanofluidic Channels for Fast Real-Time DNA
A nanometer is one-billionth of a meter, much too small to be seen with a
conventional lab microscope. This group will explore using a nanochannel that
includes a nanogap detector sensitive enough to identify DNA base pairs by
their electrical signals as a single DNA molecule is moved through the device,
eliminating the costly step of amplifying or labeling the DNA. The focus of
the initial work is to develop techniques for fabricating nanogap detectors
with improved sensitivity and functionality.
Marija Drndic, Ph.D., University of Pennsylvania, Philadelphia
$820,000 (3 years)
DNA Sequencing Using Nanopore-Nanoelectrode Devices for Sensing and Manipulation
This team of researchers will address several current obstacles to achieving
nanopore-based DNA sequencing by using nanoelectrodes to sense and manipulate
molecules passing through the nanopore, and by integrating microfluidics to
actively transport DNA molecules to the nanopore. Developments will be made
available to other groups working to create nanopore-based DNA sequencers.
Di Gao, Ph.D., University of Pittsburgh, Pennsylvania
$370,000 (2 years)
This team will lay the groundwork to prove basic principles for a technology
where DNA strands are pulled away from a solid surface when stretched by an
electric field. When the stretching force exceeds a certain value, which is
proportional to DNA length, the DNA strand would be released from the surface
and detected by fluorescence. The order in which strands are released allows
the instrument to identify the sequence of base pairs.
Xiaohua Huang, Ph.D., University of California, San Diego, La Jolla
Building on recent advances in sequencing by synthesis in several laboratories,
and this lab’s advances in preparing very large numbers of sequencing templates
on a surface, this project aims to develop an instrument and protocols to improve
DNA sequence quality and speed while lowering cost, and develop methods for genome
assembly from short sequence reads.
$2.5 million (4 years)
Genome Sequencing by Natural DNA Synthesis on Amplified DNA Clones
Jiali Li, Ph.D., University of Arkansas, Fayetteville
$830,000 (3 years)
Exploration of Solid-state Nanopore Reading Labeled Linear DNA Sequence
The goal of most nanopore-based sequencing platforms is to be able to sequence
DNA without having to label or copy the nucleotides. However, this team will
conduct basic research to develop a nanopore sensing system that labels nucleotides
with a bulky group that is easy to detect, to better differentiate the electrical
signal difference among DNA bases. The short-term goal of the method is to
determine the sequence of a piece of DNA about 1000 base pairs in length using
Stuart Lindsay, Ph.D., Arizona State University, Tempe
$370,000 (1 year)
Sequencing By Recognition
This team will test a method in which molecules that are tethered to electrodes
will bind transiently to DNA. Binding would complete an electron tunneling
circuit, signaling the presence of a particular base — A, C, G or T — within
the DNA. If successful, this method would be deployed in a nanopore with different
binding molecules for each of the four nucleotide bases.
Predrag S. Krstic, Ph.D., Oak Ridge National Laboratory, Oak Ridge,
$720,000 (2 years)
DNA Transport and Sequencing Through a Quadrupole Gate
This investigator is partnering with Mark Reed, Ph.D., of Yale University
to develop a nanoscale device that would enhance control of localization and
movement of a DNA molecule based on the idea of a quadrupole Paul trap, a component
of a mass spectrometer that confines and analyzes ions using an intermixture
of AC and DC electric fields. Ultimately, this research would combine improved
manipulation of the DNA with nucleobase detection and could potentially lead
to a cheaper alternative to nanopore sequencing.
"$100,000 Genome" Grants
NHGRI’s Near-Term Development for Genome Sequencing grants will support research aimed at sequencing a human-sized genome at 100 times lower cost than was possible when this initiative was announced in 2004. In part through the efforts of this NHGRI-led program, several technologies have recently been commercialized or are expected soon, that achieve or nearly achieve this goal. These additional grants aim for improvements that could be implemented in the near future to further enhance sequencing at this dramatically lowered cost. Grant recipients and their approximate total funding are:
Steven A. Benner, Ph.D., Foundation for Applied Molecular Evolution,
Inc., Gainesville, Florida
$1.1 million (3 years)
Near-Term Development of Reagents and
Enzymes for Genome Sequencing
This laboratory will apply innovative nucleic acid analogs and enzymes that
accept them to stepwise diminish the cost of whole genome sequencing. These
technologies, supported by bioinformatic workbenches, enable paths around
cost-generating steps by increasing the number of reactions that are run
in parallel, to prepare genomic DNA for the sequencing process.
Jingyue Ju, Ph.D., Columbia University, New York
$950,000 (2 years)
DNA Sequencing with Reversible dNTP and Cleavable Fluorescent ddNTP Terminators
This team will develop a hybrid strategy that uses a mixture of chemically
modified DNA constituents called nucleotides, along with new methods to
restart the sequencing reaction, to improve the length and quality of DNA
information produced by sequencing-by-synthesis.
Mostafa Ronaghi, Ph.D., Illumina Inc., San Diego, Calif.
$5.1 million (3 years)
Development of a 10Gb Pyrosequencer
The principal investigator of this team is an inventor of pyrosequencing,
which uses unmodified nucleotides to synthesize DNA and generate chemiluminescent
signals. Researchers plan to further develop a highly integrated and parallel
format with improved equipment for detection of the chemiluminescent signals
resulting in an approach that will enable human genome sequencing below $100,000.
For more details about the NHGRI sequencing technology development grants, go to: http://www.genome.gov/10000368.
NHGRI is one of the 27 institutes and centers at NIH. The NHGRI Division of Extramural Research supports grants for research and training and career development at sites nationwide. Additional information about NHGRI can be found at www.genome.gov.
The National Institutes of Health (NIH) — The Nation's
Medical Research Agency — includes 27 Institutes and
Centers and is a component of the U.S. Department of Health and
Human Services. It is the primary federal agency for conducting
and supporting basic, clinical and translational medical research,
and it investigates the causes, treatments, and cures for both
common and rare diseases. For more information about NIH and
its programs, visit www.nih.gov.
Note: On August 21, 2008, the quote in the second paragraph of this release was updated at the request of the institute. The original text read: "The ability to comprehensively sequence any person’s genome is the type of quantum leap needed to usher in an age of personalized medicine where healthcare providers can use an individual’s genetic code to prevent, diagnose, and treat diseases.”