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HGP and the Private Sector: Rivals or Partners?
Some people have questioned whether the publicly funded Human Genome Project (HGP) and the private sector are duplicating each others' efforts and who would "win" the race to sequence the human genome. Since the spring of 1998, when Celera Genomics announced its goal to sequence the human genome, others also have declared their intentions to sequence or map genomic regions to varying degrees.

With the June 26 announcement by the HGP and Celera Genomics that the human genome draft sequence is essentially complete, the race was declared a tie. In a sense, through its policy of open data release, HGP participants had collaborated all along in facilitating the data's use. Additionally, all HGP resources have been and are available to the research community, and the HGP actively supports projects at small companies to develop various technologies. DOE, NIH, the National Institute for Standards and Technology, and other governmental funding sources also are supporting further development and commercialization of HGP-generated resources.

Congressional Hearing
A congressional hearing before the Subcommittee on Energy and Environment of the Committee on Science of the U.S. House of Representatives in April of this year presented testimony on the importance of both sectors to future discoveries and the need for continued support of the burgeoning life sciences industry. Representatives of the U.S. Human Genome Project and Celera Genomics testified.

Robert Waterston, director of a major HGP sequencing center at Washington University, St. Louis, pointed to fruitful cooperation by the HGP and the private sector that has resulted in data sharing. Examples include (1) collaborations led by the pharmaceutical company Merck to develop partial sequences identifying genes and (2) the fruit fly sequencing project between Celera and the HGP. Examples of private-sector enrichment of public data include the SNP consortium, which involves a group of pharmaceutical companies and the Wellcome Trust philanthropy. This venture is generating a publicly available map containing human DNA variations. Most recently, a Monsanto University of Washington project generated a draft sequence of the rice plant genome, which it plans to release to the public. These efforts stand as testimony to the value of sharing data to increase knowledge for all and thus ensure future discoveries for mutual benefit.

Neal Lane (Assistant to the President for Science and Technology and Director of the Office of Science and Technology Policy) echoed the importance of partnerships between public and private sectors in his testimony to the House committee. His observations follow.

"Sequencing the genome the best-known aspect of the Human Genome Project is only the beginning of genomics," he said. "It is the first step into a future of discoveries and innovations that genomics will enable, that the public and private sectors must pursue together. . . . An expanding, evolving partnership has made human genomic discoveries possible and is now poised to make those discoveries beneficial for everyone. It is our desire to see greater collaboration between public and private sectors in all aspects of human genomics. I believe that the policies we have pursued will help to strengthen this partnership, allowing genomic discoveries and innovations to move steadily forward for the benefit of our Nation and for all humankind."

Scientific vs Commercial Goals
The public-sector HGP and private-sector companies have overlapping but not identical sequencing goals, so their "finish lines" are at different places. The HGP's commitment from the outset has been to create a scientific standard a reference genome with complete coverage of all euchromatic regions clonable with current technology and finished to the high accuracy known as Bermuda standards. Most important, all data are available freely.

Resources, technologies, and data have spurred a boom in such spin-off, publicly funded programs as the NIH Cancer Genome Anatomy Project and the DOE Microbial Genome Program. Genomes of numerous animals, plants, and microbes are being sequenced, and the number of private-sector efforts is increasing.

Most private-sector human genome sequencing projects focus on gathering enough DNA to meet their customers' needs probably in the 95% to 99% range for gene-rich, potentially lucrative genomic regions. These private data will be enriched greatly by free public-sector data containing accurate mapping (location) and sequence information. However, much data at Celera and Incyte and other genomics information based companies will remain proprietary or become available only for a fee. In addition, companies are filing numerous patent applications to stake early claims to genes and other potentially important DNA fragments.

More than the Sequence
DNA sequencing is now and will continue to be a major emphasis of the HGP for the foreseeable future. SAY WHY, IF HUMAN IS BASICALLY FINISHED. Both DOE and NIH genome programs are supporting research to develop new methods, technologies, and instruments as the basis for fully integrated, innovative approaches to rapid, low-cost determination of DNA sequence. Sequencing programs also are responsible for technology transfer from developers to users and promote collaborative, multidisciplinary projects that closely unite research work at academic and industrial laboratories.

The HGP has other important goals, including a commitment to further develop bioinformatics (computer) resources to support future research and commercial applications. The HGP also aims to explore gene function through comparative mouse-human studies, train future scientists, study human variation, and address critical societal issues arising from the increased availability of human genome data and related analytical technologies. WHAT ABOUT SNPS?

What DOE investments have improved the Human Genome Project by reducing costs, speeding progress, furthering technology?

The scientific foundation for DOE's Human Genome Initiative already existed at the national laboratories.

• DOE had a long history of conducting large multidisciplinary projects involving biologists, chemists, engineers, and mathematicians.
• Genbank, a DNA sequence repository, had been developed at Los Alamos National Laboratory (LANL) with DOE computer and data-management expertise. Today, Genbank, the world's principal DNA sequence database, resides at the National Library of Medicine.
• Chromosome-sorting capabilities essential to a genome initiative existed at LANL and Lawrence Livermore National Laboratory (LLNL). Using this technology, LANL and LLNL began the National Laboratory Gene Library Project, a collection of cloned DNAs from single human chromosomes.

In 1986, DOE became the first federal agency to announce and fund a genome program.

Developing the Tools and Technologies for Success
[NOTE: The DOE investments described below helped make the Human Genome Project the success it is today. Substantial investments by NIH and the Wellcome Trust in the U.K. were equally important, however, and should not be overlooked. In most cases, the DOE successes outlined below were the result of basic research programs. Research is an incremental process that learns from both the successes and failures of other research investments, including those at other agencies. In addition, no single instrument, technology, reagent, or protocol made high-throughput DNA sequencing possible.]

DNA Sequencers
Research on capillary-based DNA sequencing contributed to the development of the two major DNA sequencing machines currently in use—the Perkin-Elmer 3700 and the MegaBace DNA sequencers. The MegaBace DNA sequencer was developed initially with DOE funds by Dr. Richard Mathies at U.C. Berkeley. The Perkin-Elmer 3700 was based, in part, on DOE-funded research by Dr. Norman Dovichi at the University of Alberta. These high-throughput instruments are one of the keys to the current success of the genome project.

Fluorescent dyes
DNA sequencing originally used radiolabeled DNA subunits. DOE-funded research contributed to the development of fluorescent dyes that increase the accuracy and safety of DNA sequencing as well as the ability to automate the procedures.

DNA cloning vectors
Before large DNA molecules can be sequenced, they are cut into small pieces and multiplied, or cloned, into numerous copies using microbial-based "cloning" vectors. Today, the bacterial artificial chromosome (BAC) is the most commonly used vector for initial DNA amplification before sequencing. These cloning vectors were developed with DOE funds.

BAC-end sequencing
The widely agreed-upon strategy for sequencing the human genome is based on the use of BACs that carry fragments of human DNA from known locations in the genome. DOE-funded research at The Institute for Genomic Research in Rockville, Maryland, and at the University of Washington provided the sequencing community with a complete set of over 450,000 BAC-based genetic "markers" corresponding to a sequence tag every 3 to 4 kilobases across the entire human genome. These markers are needed to assemble both the draft and the final human DNA sequence.

GRAIL
GRAIL (Gene Recognition and Assembly Internet Link) is one of the most widely used computer programs for identifying potential genes in DNA sequence and for general DNA sequence analysis. This powerful analytical tool was developed with DOE funds by Dr. Ed Uberbacher at Oak Ridge National Laboratory. Although a number of gene-finding tools are now available for use, GRAIL led the way.

Reducing Costs and Speeding up Sequencing
The above technological developments have dramatically decreased DNA sequencing's cost while increasing its speed and efficiency. For example, it took 4 years for the international Human Genome Project to produce the first billion base pairs of sequence and less than 4 months to produce the second billion base pairs. The DOE sequencing team currently can generate more DNA sequence in 8 days than it did in all of 1998, its first full year of operation. Similarly, the cost of sequencing has dropped from over $2 per "finished" base to less than 10 cents during that same time. So, with fewer staff members and no budget increases, DOE currently is producing more than 30 times as much sequence as it did in 1998.

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