Faster, Cheaper Methods to Read DNA Focus on Systems Integration, Miniaturization
June 25, 1996
BETHESDA, Md. - The National Human Genome Research Institute (NHGRI) recently launched its first, full-throttle attempt to decipher human DNA - a process called DNA sequencing - by awarding funds to scientists at six U.S. institutions to begin on a pilot scale the task of spelling out the 3 billion "letters" that make up the human genetic blueprint. In parallel with these pilot DNA sequencing studies, NHGRI will award almost $13 million over the next three years to a second group of researchers to develop sequencing systems that are 10 times faster than current technologies and much cheaper than the $0.50 to $1.00 per DNA subunit, or base, it now costs.
"Current technology is good enough for starters but needs significant improvement if we are to reach our goal on time," said Dr. Francis Collins, director of NHGRI, part of the National Institutes of Health (NIH). "These research projects will push us down the path to much better sequencing technology, and help ensure the timely and cost-effective completion of theHuman Genome Project's most ambitious goal."
Since its beginning, NHGRI has supported technology development research in DNA sequencing as part of the Human Genome Project (HGP). Although methods have improved enough to begin the huge job of sequencing the human genome, further technology improvements to speed the process and reduce its cost will ensure completion of the HGP on schedule and within budget.
The technology developers plan to improve efficiency and reduce the cost of DNA sequencing by integrating all the steps in the DNA-sequencing process, making components smaller, process times shorter and requiring fewer people to run them.
The first methods for sequencing DNA were developed in the mid-1970s. At that time, scientists could sequence only a few base pairs per year. When the HGP began in 1990, few laboratories had sequenced even 100,000 DNA bases, and the cost of doing so was as high as $10 per base pair. This work has been carried out primarily using the DNA of model organisms and a technology that relies on separating and identifying each of the four DNA bases in an electrically charged gel. So far, only dedicated, large-scale sequencing laboratories are capable of sequencing even 1 million base pairs per year that way. Most of those labs sequence at a cost of about $1 per base pair, but a very few can do it for about 50 cents per base pair.
DNA sequencing is expensive and time consuming because it requires several labor-intensive steps and costly reagents. Some steps have been automated, but in most laboratories, the job from beginning to end joins a loosely connected series of operations that includes sample preparation, gel loading, running, and reading, and data assembly and vverification. While improvements have been made in individual steps, few technology developers have looked at the complete process as an integrated system; upgrading one step without improving the rest can cause bottlenecks somewhere else. Currently, for example, machines can produce sequence data much faster than they can collect and interpret the results.
"We want these investigators to follow a DNA sample from the very beginning of the process to the very end and come up with ways to make the whole process work faster and cheaper," said NHGRI's Dr. Carol Dahl, who, along with Dr. Robert Strausberg, oversees NHGRI's DNA sequencing technology development program. "The right hand will definitely have to know what the left hand is doing."
Miniaturizing sequencing components will also be a major strategy. One way to increase the rate of DNA sequencing is to scale down the size of the apparatus that performs the task. Smaller size means shorter (and quicker) travel distances for separating bases on a gel, fitting more gels in a machine, and using less of costly reagents. Some of the miniaturization approaches include capillary electrophoresis and ultra-thin gels, microfabricated devices, and micro-electro mechanical systems - tiny machines embedded on silicon chips.
The technology development projects hope to provide not only the improvements needed to complete the gargantuan human DNA sequence by the year 2005, but also a foundation for 21st-century biomedical research technology, which will rely heavily on comparing and analyzing the sequence of entire genomes from several individuals or from different species. "It will not be enough to sequence one genome and then go home," said Dr. Collins. "The technology from these projects will facilitate biomedical science beyond the year 2005 when knowledge derived from DNA sequence will underlie most experiments. Researchers and clinicians will want to analyze complete genomes from specific individuals and won't have 10 years and an international effort to do it."
Principal Investigators (award amount for three years):
Robert Brumley, GeneSys Technologies, Inc., Mazomanie, WI ($920,074):
This project will focus on integrating automated technologies for sample selection, chemical reactions, gel loading, and electrophoresis using ultra-thin gels. The researchers will use currently available robotic modules and expects to process 2 million bases of raw sequence per day, using about three people.
Mark Burns, University of Michigan, Ann Arbor ($1,326,490):
Dr. Burns's group will use photolithographic microfabrication techniques to reduce the size and improve integration and over-all cost effectiveness of components in the DNA sequencing process. This miniaturization strategy will allow measurement of nanoliter samples on microfabricated "chips," tracking samples through the system and alleviate bottlenecks.
Serge Luryi, State University of New York/Stony Brook ($1,896,415):
Efficient data collection is currently a major bottleneck in DNA sequencing. This project will address that problem using semi-conductor lasers to read fluorescently tagged DNA bases more accurately, which will reduce the need for human intervention in the data-analysis component of the process. Miniaturization techniques will allow dedicated detection for each gel lane.
Deirdre Meldrum, University of Washington, Seattle ($1,893,843):
Dr. Meldrum's project will focus on the problem of sample handling. She and her coworkers will develop methods for reducing the size and automating processing of DNA samples, which will result in reductions in amounts of reagents required, reaction times, and expense.
Philip Serwer, University of Texas Health Sciences Center, San Antonio ($428,689):
The sieving of electrophoresis gels currently allow between 300-500 bases to flow through in a single sequencing run. Enhancing gel materials to increase this number could result in significant increases in throughput. The members of this group will study gel composition and other conditions in an effort to maximize the amount of DNA that can be sequenced on a single gel.
Steven Soper, Louisana State University, Baton Rouge ($719,091):
This project seeks to develop new, automated methods for handling very small (nanoliter) DNA samples at the beginning stages of the sequencing process. This step will be interfaced with a capillary electrophoresis system. Using nanoliter volumes of sample promises to reduce expense by requiring less reagent.
David States, University of Washington, Seattle ($360,834):
While technology improvements are making DNA sequencing machines produce more data quicker, computer scientists need to develop methods capable of collecting and analyzing the increase. Dr. States and his group will study the impact of scale up on data handling, and develop computer programs to keep pace with new sequencing technologies. They will work in collaboration with the genome sequencing center at Washington University in St. Louis.
James Weber, Marshfield Medical Research Foundation, WI ($475,951):
Marshfield is the home of the scanning fluoresence detecting device, SCAFUD, which will be ramped up in this project from an output rate of 63 million bases per year to 215 million. The 3.5-fold increase in capability will be achieved through a number of hardware and software improvements.
Gregory Went, CuraGen Corporation, Branford, CT ($4,868,102):
This collaborative effort between Curagen Corporation, Soane BioSciences, and the genome center at the Whitehead Insititute for Biomedical Research, will develop a novel fluorescent sequencing and software analysis system based on ultra-thin electrophoresis gels. The system will be compatible with existing high-throughput instruments for preparing DNA samples.
National Human Genome Research Institute
Last Reviewed: February 25, 2012