New Grants Bolster Efforts to Generate Faster and Cheaper Tools for DNA Sequencing
News Aug 02, 2007
Looking ahead to a future in which each person’s genome can be sequenced as a routine part of medical research and health care, the National Human Genome Research Institute (NHGRI), part of the National Institutes of Health (NIH), has awarded more than $15 million in grants to support development of innovative technologies with the potential to dramatically reduce the cost of DNA sequencing.
"Innovative sequencing technologies are critical to our efforts to move advances in genomic knowledge into the clinic. The era of personalized medicine will demand more efficient and cost-effective approaches to DNA sequencing,” said NHGRI Director Francis S. Collins, M.D., Ph.D.
DNA sequencing costs have fallen more than 50-fold 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. However, it still costs as much as $5 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, allowing 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 will fund eight investigators 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. 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.
"The different approaches will likely result in several successful and complementary technologies. We will monitor carefully to see how each technology progresses and which of them can ultimately be used by the average researcher or health care provider,” said Jeffery Schloss, Ph.D., NHGRI's program director for technology development. "Each research team brings a unique set of skills and expertise to solving difficult scientific and engineering problems."
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:
• Richard B. Fair, Ph.D., Duke University, Durham, N.C.
$3,686,000 (3 years)
Continuous Sequencing-by-Synthesis, Based on a Digital Microfluidic Platform
- This group has already shown the potential of droplet-based microfluidics in sequencing-by-synthesis. Their new goals are to extend read length, minimize reaction volume and increase throughput to 10,000 reactions in a very small area. Separating the chemistry and detection steps makes this technology more efficient, and the droplet-based microfluidics system solves many of the difficulties involved with complicated fluid handling on a very small scale.
• Stuart Lindsay, Ph.D., Arizona State University, Tempe
$877,000 (3 years)
Sequencing by Recognition
- A nanometer is one-billionth of a meter, much too small to be seen with a conventional lab microscope. 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. This research team seeks to develop molecular wires that are sufficiently flexible and sensitive to enable this type of sequencing.
• Xinsheng Sean Ling, Ph.D., Brown University, Providence, R.I.
$820,000 (3 years)
Hybridization-Assisted Nanopore DNA Sequencing
- Investigating further the potential of nanopore technology, these researchers intend to use solid-state nanopores to detect the location, along a DNA strand, where another short, known DNA sequence attaches by hybridization (base-pairing). By doing this experiment many times with many different short, known sequences, the sequence of long DNA strands would be determined.
• Wlodek Mandecki, Ph.D., University of Medicine and Dentistry of New Jersey, Newark
$1,672,000 (3 years)
Ribosome-Based Single Molecule Method to Acquire Sequence Data from Genomes
- This researcher and his team will modify key components of the ribosome — the translation system that cells use to build proteins on messenger RNA templates — to read out the sequence of nucleotide building blocks along that message. Any DNA molecule can be converted to such a message, so by “sequencing” the messenger RNA, the sequence of the DNA itself could be determined.
• Andre Marziali, Ph.D., University of British Columbia, Vancouver
$746,000 (3 years)
Nanopore Array Force Spectroscopy Chip for Rapid Clinical Genotyping
- These investigators will develop solid-state, nanopore-based force spectroscopy for rapid electronic detection of sequence variation. The project builds on the team’s previous demonstration of the ability to detect sequences at single base resolution using organic nanopore force spectroscopy.
• John S. Oliver, Ph.D., NABsys, Inc., Providence, R.I.
$498,000 (2 years)
Hybridization-Assisted Nanopore Sequencing
- This team will work with collaborators at Brown University to develop the biochemical and algorithmic components of a method for sequencing by hybridization. By designing tagged probes and novel reconstruction algorithms, the team expects to get around the resolution limits that have prevented nanopores from being used for sequencing.
• Robert Riehn, Ph.D., North Carolina State University, Raleigh
$439,000 (2 years)
Sequencing DNA by Transverse Electrical Measurements in Nanochannels
- This group proposes to stretch long DNA molecules by passing them through nanofluidic channels. Nanoelectrodes will be built into those channels to detect each DNA base’s specific electrical signal.
• H. Kumar Wickramasinghe, Ph.D., University of California, Irvine
$2,184,000 (3 years)
High-Throughput, Low-Cost DNA Sequencing Using Probe Tip Arrays
- This group has proven the feasibility of accelerating and miniaturizing the conventional Sanger method of DNA sequencing by relying on nano-scale electrophoretic separation of DNA fragments along the surface of an Atomic Force Microscope probe tip. This method reduces volume of materials, potentially accelerating and reducing the cost of sequencing. Researchers plan to demonstrate these very challenging separations and to implement them on a massively parallel sequencing platform containing hundreds of probe tips.
“$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 either recently been commercialized, or are expected to be released during the next few months, that have great potential to achieve this goal.
These additional grants aim to make improvements that could be implemented in the near future to further improve sequencing at this dramatically-lowered cost. Grant recipients and their approximate total funding are:
• Jeremy S. Edwards, Ph.D., University of New Mexico School of Medicine, Albuquerque
$900,000 (3 years)
Polony Sequencing the Human Genome
- The ultimate goal of this team is to use established polony genome sequencing technology to re-sequence a human genome within a week for less than $10,000. To meet their goal, they will continue improving the quality of sequencing data and further develop the computational tools needed to assemble a human genome sequence.
• Jingyue Ju, Ph.D., Columbia University, New York (Two Grants)
$644,000 (2 years)
3’-O-Modified Nucleotide Reversible Terminators for Pyrosequencing
- This investigator will design a library of synthetic molecular tools designed to optimize the pyrosequencing method to overcome the difficulties deciphering repetitive regions of DNA templates. The current pyrosequencing method utilizes unmodified DNA base pairs and polymerases to synthesize DNA and a firefly enzyme to generate a chemiluminescent signal.
• $2,217,000 (2 years)
An Integrated System for DNA Sequencing by Synthesis
- This team will continue its development and optimization of a novel set of fluorescent nucleotide reversible terminators for sequencing by synthesis. A new method for preparing DNA-beads for attachment to a substrate will also be developed. The goal is to increase the length of the DNA sequencing reads while maintaining high data quality.
• David C. Schwartz, Ph.D., University of Wisconsin, Madison
$882,000 (3 years)
Sequence Acquisition from Mapped Single DNA Molecules
- The focus of this project is to create a system capable of analyzing large amounts of human genome data that ties the location of sequence elements to longer-range map information. This would include information such as structural variations and aberrations associated with cancer genomes. The resulting data could be linked to information produced by other emerging sequencing platforms.
As genome editing technologies advance toward clinical therapies, they are raising hopes of a completely new way to treat disease. However, challenges need to be addressed before potential treatments can be widely used in patients. To tackle these challenges, the National Institutes of Health has launched the Somatic Cell Genome Editing program, which has awarded multiple grants including more than $3.6 million to assess the safety of genome editing in human cells and tissues.