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NHGRI aims to make DNA sequencing faster, more cost effective

The National Human Genome Research Institute (NHGRI), part of the National Institutes of Health (NIH), today announced the latest round of grant awards totaling more than $13 million to speed the development of innovative sequencing technologies that reduce the cost of DNA sequencing and expand the use of genomics in medical research and health care.

"There has been significant progress over the last several years to develop faster and more cost-effective sequencing technologies and, we are committed to supporting these innovative efforts to benefit scientific labs and medical clinics," said NHGRI Director Francis S. Collins, M.D., Ph.D. "These technologies will eventually revolutionize the way that biomedical research and the practice of medicine are done."

Since 1990, NHGRI has invested approximately $380 million to develop and improve DNA sequencing technologies. 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 project to sequence the human genome. However, it still costs around $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, allowing researchers to sequence the genomes of hundreds or even thousands of people participating in 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 an individual's genome during 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 nine investigators developing revolutionary technologies that may make it feasible to sequence a genome for $1,000, as well as two investigators developing "near 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. Since 2004, NHGRI has awarded $83 million to investigators to develop both "near term" and revolutionary sequencing technologies.

"It is very important that we encourage and support the development of innovative sequencing technologies. Many of these new approaches have shown significant promise, yet far more exploration and development are needed if they are to be useful to the average researcher or physician," said Jeffery Schloss, Ph.D., NHGRI's program director for technology development. "We look forward to seeing which of these technologies fulfill their promise and achieve the quantum leaps that are needed to take DNA sequencing to the next level."

"$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:

  • John Nelson, Ph.D., General Electric Global Research, Niskayuna, N.Y.,$900,000 (2 years),"Closed Complex Single Molecule Sequencing"

This team will use existing enzyme and dye-tagged nucleotide resources, the building block of DNA, in a novel way that will simplify the fundamental, front-end chemistry of massively parallel sequencing-by-synthesis. This method uses the natural catalytic cycle of DNA polymerase to capture just a single DNA base on an immobilized primer/template. A fluorescence scanner will be used to scan and identify hundreds of thousands of molecules at once. Then the cycle will be repeated. Thi s phased award will increase if specific milestones are met in the initial experiments.

  • J. Michael Ramsey, Ph.D., University of North Carolina, Chapel Hill,$3.8 million (4 years),"Nanoscale Fluidic Technologies for Rapidly Sequencing Single DNA Molecules"

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 2 nanometers in diameter) for use as DNA sequence transducers and propose to detect an electrical, or ionic, signal from individual DNA molecules. The goal of this group is to fabricate nanoscale channels in which single molecules of DNA will pass between nano-electrodes that are less than 2 nanometers apart, to measure an electric current that will identify individual bases.

  • Xiaohua Huang, Ph.D., University of California, San Diego, La Jolla,$275,000 (1 year),"Genome Sequencing by Ligation Using Nano-Arrays of Single DNA Molecules"

Using an experimental method for DNA sequencing called "single molecule sequencing by ligation," this project aims to develop a method for fabricating high-density arrays of wells with sub-micrometer dimensions for ordering single nanoparticles and DNA molecules. The investigator will attempt to demonstrate that more than 1 billion individual DNA molecules can be sequenced in massive parallel though a process involving cyclic sequencing by ligation, a process where an enzyme is used to join pieces of DNA together. This phased award will increase if specific milestones are met in the initial experiments.

  • Amit Meller, Ph.D., Boston University, Boston,$2.2 million (3 years),"High-Throughput DNA Sequencing Using Design Polymers and Nanopore Arrays"

This group along with their industrial partner LingVitae AS, will continue to implement a novel approach previously funded through this program in which a nanopore is used to simultaneously detect electrical and fluorescent signals from many nanopores at one time. A novel sequencing instrument will be fabricated, along with additional analysis tools, with the aim of producing a viable, low-cost sequencing system.

  • Timothy D. Harris, Ph.D, Helicos Biosciences Corporation, Cambridge, Mass.,$2 million (3 years),"High Accuracy Single Molecule DNA Sequencing by Synthesis"

This team of investigators has developed a fully automated instrument capable of sequencing single molecules of DNA on a planar surface. The group is now developing a high-throughput version of this technology for the re-sequencing of whole human genomes. The sequencing strategy involves obtaining short reads (about 25 DNA bases) from billions of strands of DNA immobilized on a surface inside a reagent flow cell. The research plan aims to advance this strategy to achieve high accuracy, re-sequencing of highly variable genomes and assembly of never-before sequenced genomes.

  • Dmitri V. Vezenov, Ph.D., Lehigh University, Bethlehem, Penn. ,$905,000 (3 years),"Force Spectroscopy Platform for Label Free Genome Sequencing"

This team will apply force spectroscopy, a technique used to understand the mechanical properties of polymer molecules or chemical bonds, to DNA undergoing arrested polymerization to initially demonstrate one-molecule-at-a-time analysis of changes in molecular mechanics at a resolution of a single base. Using optical, near-field probes, the methods of force spectroscopy can be advanced into techniques having massively parallel format, where millions of single DNA base additions can be followed at the same time. The identification of bases will be done exclusively on the basis of changes experienced by the molecule as a whole. The team aims to fabricate a low cost table-top setup suitable for use in a majority of biological, chemical and hospital laboratories.

  • Peiming Zhang, Ph.D., Arizona State University, Tempe, Ariz.,$8 95,000 (3 years),"Fabrication of Universal DNA Nanoarrays for Sequencing by Hybridization"

Expanding the performance of the sequencing-by-synthesis technology, this group will develop a cost-effective method to fabricate universal DNA nanoarrays using nano-contact printing. The current photolithography technology can cause damage to DNA probes, which the group will strive to avoid by using nano-contact printing. With the nano-sized features, a DNA nanoarray can also improve throughput by offering the ability to accommodate billions of DNA molecules in a small area. Hybridization will be detected by atomic force microscopy.

  • Carlos H. Mastrangelo, Ph.D., Case Western Reserve University, Cleveland,$815,000 (3 years),"Large-Scale Nanopore Arrays for DNA Sequencing"

This team will aim to develop highly integrated arrays of nanopores that can be fabricated by lithographic methods, along with on-chip silicon-based electronic circuits and circuit techniques that amplify and isolate their various electrical signals. This group will also design a dipole-sensing methodology, which in principle can distinguish signals from each of the DNA bases. Arrays of nanopores will be constructed on silicon substrates using a self-aligned compositional approach. Quadrature dipole moment detectors will be constructed that yield a signal independent of the rotation of the DNA molecule relative to the electrodes.

  • Jens Gundlach, Ph.D., University of Washington, Seattle,$605,000 (2 years),"Engineering MspA for Nanopore Sequencing"

The passage of single-strand DNA through a nanometer-scale pore is driven by an electric field revealing information about the DNA sequence. This method has the potential to become an inexpensive, ultrafast DNA sequencing technique. Most nanopore sequencing approaches involve either the protein pore alpha-hemolysin or artificial pores in inorganic materials. This team will use protein-engineering to tailor an alternative protein pore, Mycobacterium smegmatis porin A (MspA), for 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 is possible today. There is strong potential that, in less than five years, several of these technologies will be at or near commercial availability. Grant recipients in the current cycle and their approximate total funding are:

  • Michael L. Metzker, Ph.D., Human Genome Sequencing Center, Baylor College of Medicine, Houston,$500,000 (1 year),"Ultrafast SBS (Sequencing by Synthesis) Method for Large-Scale Human Resequencing"

This team has developed a novel type of fluorescent nucleotide that is modified for sequencing by synthesis. Their goal is to improve the chemical subunits, called reversible terminators, for use in a system that will ultimately be used to sequence DNA templates in high-density arrays, using a sensitive fluorescence detection system.

  • Steven Jeffrey Gordon, Ph.D., Intelligent Bio-Systems, Inc., Worcester, Mass.,$425,000 (1 year),"High-Throughput DNA Sequencing by Synthesis Platform"

The main goal of this project is to develop a high-speed, massively parallel DNA sequencing system using unique base analogues and the sequencing by synthesis approach, in collaboration with a group at Columbia University. This application is focused on the development of the subsystems required to construct high-density sample arrays on glass chips and to run sequencing by synthesis reactions on them in an automated, high-throughput fashion.


Source:NIH/National Human Genome Research Institute

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