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HGP and the Private Sector

The Human Genome Project & the Private Sector

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L-R: Venter, Patrinos, Collins
Craig Venter (former head of Celera Genomics), Ari Patrinos (director of DOE Human Genome Program and Biological and Environmental Research Program), and Francis Collins (director, NIH National Human Genome Research Institute).

On the Shoulders of Giants: Private Sector Leverages HGP Successes
Data, Technologies Catalyze a New, High-Profile Life Sciences Industry

The deluge of data and related technologies generated by the Human Genome Project (HGP) and other genomic research presents a broad array of commercial opportunities. Seemingly limitless applications cross boundaries from medicine and food to energy and environmental resources, and predictions are that life sciences may become the largest sector in the U.S. economy.

Established companies are scrambling to retool, and many new ventures are seeking a role in the information revolution with DNA at its core. IBM, Compaq, DuPont, and major pharmaceutical companies are among those interested in the potential for targeting and applying genome data.

In the genomics corner alone, dozens of small companies have sprung up to sell information, technologies, and services to facilitate basic research into genes and their functions. These new entrepreneurs also offer an abundance of genomic services and applications, including additional databases with DNA sequences from humans, animals, plants, and microbes.

Other applications include gene fragments to use for drug development and target identification and evaluation, identification of candidate genes, and RNA expression information revealing gene activity. Products include protein profiles; particular genotypes associated with such specific medically important phenotypes as disease susceptibility and drug responsiveness; hardware, software, and reagents for DNA sequencing and other DNA-based tests; microarrays (DNA chips) containing tens of thousands of known DNA and RNA fragments for research or clinical use; and DNA analysis software.

Broader applications reaching into many areas of the economy include the following:

  • Clinical medicine. Many more individualized diagnostics and prognostics, drugs, and other therapies.
  • Agriculture and livestock. Hardier, more nutritious, and healthier crops and animals.
  • Industrial processes. Cleaner and more efficient manufacturing in such sectors as chemicals, pulp and paper, textiles, food, fuels, metals, and minerals.
  • Environmental biotechnology. Biodegradable products, new energy resources, environmental diagnostics, and less hazardous cleanup of mixed toxic-waste sites.
  • DNA fingerprinting. Identification of humans and other animals, plants, and microbes; evolutionary and human anthropological studies; and detection of and resistance to harmful agents that might be used in biological warfare.

From the start, HGP planners anticipated and promoted the private sector's participation in developing and commercializing genomic resources and applications. The HGP's successes in establishing an infrastructure and funding high-throughput technology development are giving rise to commercially viable products and services, with the private sector now taking on more of the risk.

A Public Legacy

Substantial public-sector R&D investment often was needed in feasibility demonstrations before such start-up ventures as those by Celera Genomics, Incyte, and Human Genome Sciences could begin. In turn, these companies furnished valuable commercial services that the government could not provide, and the taxes returned by their successes easily repay fundamental public investments. Following are a few key public R&D contributions that made some current genomics ventures commercially feasible. These examples describe DOE investments, but substantial commitments by NIH and the Wellcome Trust in the United Kingdom were equally important.

Scientific Infrastructure. The scientific foundation for a human genome initiative existed at the national laboratories before DOE established the first genome project in 1986. Besides expertise in a number of areas critical to genomic research, the laboratories had a long history of conducting large multidisciplinary projects.

Genomic Science and Pioneering Technology. GenBank, the world's DNA sequence repository, was developed at Los Alamos National Laboratory (LANL) and later transferred to the National Library of Medicine. Chromosome-sorting capabilities developed at LANL and Lawrence Livermore National Laboratory enabled the development of DNA clone libraries representing the individual chromosomes. These libraries were a crucial resource in genome sequencing.

Sequencing Strategies. When the HGP was initiated, vital automation tools and high-throughput sequencing technologies had to be developed or improved. The cost of sequencing a single DNA base was about $10 then; by 2001, sequencing costs had fallen about 100-fold to $.10 to $.20 a base and still are dropping rapidly.

DOE-funded enhancements to sequencing protocols, chemical reagents, and enzymes contributed substantially to increasing efficiencies. The commercial marketing of these reagents has greatly benefitted basic R&D, genome-scale sequencing, and lower-cost commercial diagnostic services.

Sequencing Technologies and Biological Resources. Other major factors in cost and time reduction were greatly improved sequencing instruments and efficient biological resources such as the following:

  • DOE-funded research on capillary-based DNA sequencing contributed to the development of the two major sequencing machines. The core optical system concept of the Perkin-Elmer 3700 sequencing machine (used by Celera and others) was pioneered with DOE support. The instrumentation concepts that matured as the MegaBACE sequencer were pioneered by Richard Mathies (University of California, Berkeley). The DOE JGI chose this sequencing hardware platform after competitive trials.
  • DNA sequencing originally was done with radiolabeled DNA fragments. Today, DOE improvements to fluorescent dyes decrease the amount of DNA needed and increase the accuracy of sequencing data.
  • Bacterial artificial chromosome (BAC) clones, developed in the DOE program, became the preferred starting resource in sequencing procedures because of their superior stability and large size. A critical component of public- and private-sector sequencing, BACs were used to assemble both the draft and final human DNA reference sequences.
  • Further extending the usefulness of BACs, the DOE HGP funded the production of sequence tag connectors (STCs) from BAC ends. This early information enabled the selection of optimal BACs for complete sequencing, thus saving time and money. STC use for the HGP was advocated by Craig Venter and Nobelist Hamilton Smith (Celera), and Leroy Hood (now at the Institute for Systems Biology).

A Successful Transformation

These successes transferred much of the repetitive labor from humans to automated machines. In addition, new software for data processing both alleviated and sped human decision making. Over the last decade, advances in instrumentation, automation, and computation have transformed the entire process. Further innovations, however, still are needed for completing many large sequences and increasing the effectiveness of sequencing.

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HGP and the Private Sector: Rivals or Partners?

With the June 26, 2000, announcement by the publicly funded Human Genome Project (HGP) and Celera Genomics that the draft sequence of the human genome was essentially complete, the complementary aspects of the public and private sectors sequencing projects were realized.

After the spring of 1998, when Celera Genomics announced its sequencing goal, other private companies also declared their intention to sequence or map genomic regions to varying degrees. Some people questioned whether the HGP and the private sector were duplicating work, and they wondered who would win the race to sequence the human genome. Although the HGP and private companies did have overlapping sequencing goals, their finish lines were different because their ultimate goals were not the same.

In a sense, through its policy of open data release, the HGP has all along facilitated the research of others. Additionally, the HGP funds projects at small companies to devise needed technologies. DOE, NIH, the National Institute for Standards and Technology, and other governmental funding sources also supported further application and commercialization of HGP-generated resources.

HGP products spurred a boom in such spin-off 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 endeavors is increasing. Technology transfer from developers to users and participation in collaborative, multidisciplinary projects closely unite researchers at academic, industrial, and governmental laboratories.

Scientific vs Commercial Goals

The HGP's commitment from the outset was to create a scientific standard (an entire reference genome). Most private-sector human genome sequencing projects, however, focused on gathering just enough DNA to meet their customers' needs—probably in the 95% to 99% range for gene-rich, potentially lucrative regions. Such private data continue to be enriched greatly by accurate free public mapping (location) and sequence information. Celera's shotgun sequencing strategy, for example, created millions of tiny fragments that had to be ordered and oriented computationally using, in part, HGP research results. Most data at Celera, Incyte, and other genomics information-based companies are proprietary or available only for a fee. In addition, companies are filing numerous patent applications to stake claims to genes and other potentially important DNA fragments.

More than the Reference Sequence

DNA sequencing will continue to be a major emphasis for the foreseeable future as gene sequences are surveyed across various populations. Both the DOE and NIH genome programs continue to support the development of fully integrated and innovative approaches to rapid, low-cost sequencing.

Other HGP goals from the final 5-year plan were to enhance bioinformatics (computational) resources to support future research and commercial applications. The HGP also aimed 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.

Congressional Hearing Explored Controversies, Benefits of Public Genome Project
Why was a public project needed if the work could be done in the private sector?

In April 2000 the Subcommittee on Energy and Environment of the Committee on Science of the U.S. House of Representatives conducted hearings on the status and benefits of genome sequencing in the public and private sectors. Speakers included representatives of the U.S. HGP and Celera Genomics, members of Congress, and the director of the Office of Science and Technology Policy.

Robert Waterston, directory of the HGP sequencing center at Washington University, St. Louis, pointed to fruitful data sharing by the HGP and the private sector. Examples included (1) collaborations led by the pharmaceutical company Merck to develop partial sequences identifying genes and (2) the fruit fly sequencing project by Celera and the HGP.

Examples of private-sector enrichment of public data included the SNP consortium, which generated a publicly available map containing human DNA variations. (See article.) In September 2000, Celera Genomics announced a reference database with more than 2.8 million unique SNPs, including those screened from public-sector databases. In October a public-private consortium announced the joint sequencing of the laboratory mouse. (See article.) Also, a Monsanto-University of Washington project generated a draft sequence of the rice plant genome for release to the public. These efforts show the value of sharing data to increase knowledge and ensure future discoveries for mutual benefit.

Neal Lane (formerly 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 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...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."

More Information

Human Genome Project 1990–2003

The Human Genome Project (HGP) was an international 13-year effort, 1990 to 2003. Primary goals were to discover the complete set of human genes and make them accessible for further biological study, and determine the complete sequence of DNA bases in the human genome. See Timeline for more HGP history.

Human Genome News

Published from 1989 until 2002, this newsletter facilitated HGP communication, helped prevent duplication of research effort, and informed persons interested in genome research.