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), has awarded more than $20 million in grants to develop 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 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," 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, Mass.
$6.5 Million (4 Years)
Electronic Sequencing In Nanopores
 
Several groups are developing nanopores 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 Sequencing

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) DNA Sequencing-at-a-Stretch

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
$2.5 Million (4 Years)
Genome Sequencing by Natural DNA Synthesis on Amplified DNA Clones
 
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.

• 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 solid-state nanopores.

• 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, Tenn.
$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.