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The Road to the $1000 Genome — A Roundup of Sequencing Technology Developments

August 2010
DNA illustration. Image courtesy of Robert Johnson, University of Pennsylvania.

Recent news articles marking the tenth anniversary of the announcement of the first draft sequence of the human genome also predicted the rise of DNA sequencing technologies that sequence a human genome for $1,000 or less in the next three to five years, a development that would change the face of biomedical research and clinical practice.

The effort to bring the cost of high-quality human genome sequencing down to $1,000 or less began in 2004 with the award of the first grants from the National Human Genome Research Institute's (NHGRI) Advanced DNA Sequencing Technology Program. At the time, Sanger sequencing employed during the Human Genome Project, using 100 machines over three to four months , produced a high-quality draft of a human or mammalian-sized genome for about $10 million.

The initial five-year goal of the program was to develop second, or next generation (NextGen) sequencing technologies that could reduce the cost of sequencing a human genome by two orders of magnitude to $100,000. That sequencing goal has been met and surpassed, thanks in part to the NHGRI program and other academic and private efforts. Such efforts have miniaturized the technologies that use exponentially less of the expensive chemical reagents needed in the first generation sequencing machines, and perhaps more importantly, are able to simultaneously read millions of sequencing reactions rather than just hundreds.

With NextGen DNA sequencing technologies being used in laboratories today, the cost of sequencing a human genome is now about $20,000, and sequencing can be completed with one machine in about a week because these machines process more than 100 million samples a run. Still, getting from a $10,000 genome sequence to a $1,000 genome sequence will not be a trivial endeavor.

For that reason, NHGRI continues to fund the development of revolutionary sequencing technologies. In 2009, NHGRI awarded approximately $19 million to 10 sequencing technology development projects. In addition, NHGRI named as its Recovery Act signature project the development of third generation sequencing technologies (3Gen), able to sequence an individual human genome for $1000. Seven additional projects were awarded more than $13 million in Recovery Act funds to further accelerate these efforts.

This article is the first in a series of periodic updates that will summarize breakthroughs recently published in the scientific literature by NHGRI-funded researchers who address or overcome obstacles to developing revolutionary 3Gen sequencing technologies.

Such efforts will integrate engineering with biochemistry, chemistry, nanotechnology and physics to enhance breakthrough DNA sequencing and analysis technologies. The expected result will be solutions to the analytical challenges researchers face in achieving the goal of a $1,000 genome.

"For example, one type of innovation our grantees are developing would eliminate the current need for expensive optical systems and other custom reagents," said Jeffery Schloss, Ph.D., NHGRI's program director for Genome Technology Development, "It's important to explore a wide range of innovative approaches. Instead of using fluorescence to identify DNA base pairs, some groups we fund are designing a technology that could feature a chip containing thousands to millions of nanopores."

A nanopore is a hole about two nanometers in diameter. One nanometer is one-billionth of a meter.

"As the DNA molecule passes through the nanopore, base pairs are detected electronically depending on size and chemistry," added Dr. Schloss. "While we are not there yet, we are seeing several technologies that will bring us to a $1000 human genome."

Many current NextGen sequencing platforms are multifunctional, able to not only sequence DNA, but to perform other analyses on cells and DNA molecules. The same functions, with marked improvements, will also need to be developed in 3Gen sequencing platforms.

For example, the ability to conduct gene expression profiles on a small number of cancer cells using 3Gen is an area of high interest for biomedical and clinical researchers, who seek early diagnosis and prevention of the disease.

A team that includes researchers from Helicos BioSciences Corporation in Cambridge, Mass., has demonstrated a way to generate digital gene-expression profiles from a minute quantity of cells using the company's single molecule sequencing technology, developed with prior funding from NHGRI's Advance DNA Sequencing Technology program. Helicos has also received a Recovery Act grant to improve their sequencing technology to produce a $1,000 genome.

The authors, who published their finding online on July 18, 2010 in Nature Methods, were able to capture and differentiate gene expression profiles when as few as 250 cells were processed. And they did so without the multiple amplification and manipulation steps required by NextGen methods. Still, the authors cautioned that the present method they employed will need to be further optimized to improve efficiency to a level that achieves reliable single-cell analyses.

Another critical function of future DNA sequencing technologies is the ability to detect DNA methylation patterns in the epigenome — those chemical markers on DNA that play a central role in normal development as well as diseases such as cancer.

Publishing online on May 9, 2010 in Nature Methods, Stephen Turner, Ph.D., Chief Technology Officer for Pacific Biosciences, Inc., of Menlo Park, Calif., the principal investigator of a Recovery Act grant from NHGRI, and his team reported they have developed a proof-of-principle method to detect DNA methylation patterns using their Single Molecule Real Time sequencing technology. The findings illustrate the potential of the Pacific Biosciences sequencing platform to be adapted for other uses beyond DNA sequencing.

One constraint of NextGen sequencing, which analyzes DNA molecules by chopping them into tiny pieces only a few thousand "letters" long, is its limited ability to detect large-scale genetic variation where thousands to hundreds of thousands of DNA letters can be inserted randomly, repeated or deleted in the genome, leading to disease. The capacity to detect such large-scale genetic variation is a challenge for 3Gen sequencing technologies.

At the University of Wisconsin-Madison (UW), David Schwartz, Ph.D., and his team have been developing their Optical Mapping System to comprehensively study large-scale variations and their role in human health and disease. The genome mapping system is able to analyze large DNA molecules one at a time, reducing the number of DNA pieces that need to be put back together in the analysis. This allows researchers to look at these large genetic changes across an entire individual's genome.

The UW team recently tested the Optical Mapping System to measure its ability to analyze large genetic variation in four human genomes. The system was able to detect inversions, deletions and other large genetic variations ranging from about three thousand to millions of DNA base pairs. They also identified more than 4,000 unique large variants across the four genomes. The results are published in the June 15, 2010 issue of the Proceedings of the National Academy of Sciences.

Several groups funded by NHGRI are developing the nanopore-based sequencing technologies Dr. Schloss described above. Such technologies, in theory, will be able to sequence a human genome using small hand-held devices in less than a day.

Marija Drndic, Ph.D., and colleagues at the University of Pennsylvania have developed a nanopore system fabricated using graphene membranes, a very thin sheet of uniquely arranged carbon atoms on the order of 1-5 nanometers, to electrically detect single DNA molecules. Their findings, published online on July 23 in Nano Letters, offer early experiments demonstrating that passing DNA through graphene nanopores can be electronically measured. This material is particularly interesting because it might be used as both the nanopore and the electrical connection, making it easier to build sequencing devices.

A research team from Boston University, led by Amit Meller, Ph.D., has demonstrated an optically-based method for DNA sequence readout combined with a nanopore system that allows them to probe multiple pores simultaneously using a single fast digital camera. The results were published online on May 11 in Nano Letters.

Other versions of nanopore sequencing technologies appear to be on the brink of making the quantum leap needed to achieve a $1000 genome because they don't use chemicals, but rely on electric signals, which also may bypass the need for major data storage required by the large imaging files associated with NextGen platforms.

In the process of developing nanoscale DNA sequencing technologies, researchers are also working to understand the optimal way to move a DNA molecule through a nanopore so they can advance these technologies. Murugappan Muthukumar, Ph.D., at the University of Massachusetts, Amherst, is taking on this important and challenging task. He recently published a theory on the average travel time of a polymer (a DNA molecule is classified as a polymer) passing through a nanopore when exposed to an electric field. This is important because the DNA molecule needs to be captured by, and then pass through the nanopore at an optimal speed to accurately detect DNA base pairs. His theory was published online in The Journal of Chemical Physics on May 17, 2010.

Regardless of the sequencing technologies that will break the $1000 cost barrier in the next few years, these efforts, and those of other NHGRI grantees in the Advanced DNA Sequencing Technology Development program, will contribute in unique ways to bringing routine human genome sequencing closer to reality.

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Last Reviewed: April 11, 2011

Last updated: April 11, 2011