J. Craig Venter Institute
The J. Craig Venter Institute (JCVI) is a non-profit genomics research institute founded by J. Craig Venter, Ph.D. in October 2006. The Institute was the result of consolidating four organizations: the Center for the Advancement of Genomics, The Institute for Genomic Research (TIGR), the Institute for Biological Energy Alternatives, and the J. Craig Venter Science Foundation Joint Technology Center. It has facilities in Rockville, Maryland and La Jolla, California.
The Institute studies the societal implications of genomics in addition to genomics itself. The Institute's research involves genomic medicine; environmental genomic analysis; clean energy; synthetic biology; and ethics, law, and economics. The Institute employs over 400 people, including Nobel laureate Hamilton Smith.
The pre-history of JCVI is deeply entwined with the race to sequence the human genome. Craig Venter was a researcher at the National Institutes of Health (NIH), and had started The Institute for Genomic Research (TIGR), a nonprofit private research institute, in 1992 to work on various sequencing projects, including the Human Genome Project (HGP). Among the various accomplishments of TIGR was the first complete genomic sequencing of a free living organism, Haemophilus influenzae, in 1995. This used a shotgun sequencing technique pioneered earlier, but which had never been used for a whole bacterium until TIGR's project.
Venter vocally disagreed with the manner in which the HGP project was being managed, and in 1998, TIGR found itself excluded from the U.S. HGP groups selected for continued funding by NIH. In May 1998, Venter announced that he was quitting the HGP and had joined with investors to start a commercial venture, Celera, which would produce the complete genome sequence in three years – seven years' less time than the HGP timetable. The costs of the sequencing effort would be recovered by marketing the sequences, which would be held in a proprietary database as intellectual property protected by patent. Dozens of other companies including Incyte Pharmaceuticals and Human Genome Sciences also began patenting sequences.
To many researchers, the thought of gene patenting was anathema. They worried about a future in which they would need to secure dozens of licenses from private firms before they could conduct research. To them, the notion of patenting a naturally occurring substance violated common sense. In response to their outcry, the NIH massively increased the pace of its own sequencing endeavours, adopting several of the strategies that Venter had announced that he was using to expedite Celera's sequencing campaign. The political, personal, and ethical conflicts of the race between the public and private sectors in this effort have been documented in numerous books and articles.
TIGR, meanwhile, continued its own list of accomplishments. TIGR scientist Claire Fraser led the projects to sequence the second bacterium, Mycoplasma genitalium in 1995, and less than a year later TIGR's Carol Bult led the project to sequence the first genome of an Archaeal species, Methanococcus jannaschii. TIGR followed these accomplishments with the genomes of the pathogenic bacteria Borrelia burgdorferi (which causes Lyme Disease) in 1997 and Treponema pallidum (which causes syphilis) in 1998. In 1999 TIGR published the sequence of the radioresistant polyextremophile Deinococcus radiodurans. TIGR eventually sequenced and analyzed more than 50 microbial genomes. Its bioinformatics group developed many of the pioneering software algorithms that were used to analyze these genomes, including the automatic gene finder GLIMMER and the sequence alignment program MUMmer.
Following the 2001 anthrax attacks, TIGR partnered with the National Science Foundation and the FBI to sequence the strain of Bacillus anthracis used in those attacks. The results of this analysis were published in the journal Science in 2002. The genetic evidence was later credited by the FBI with helping to pinpoint the precise sample of anthrax bacteria, from a lab in Fort Detrick, Maryland, that was the source of the attacks.
After the race to sequence a draft human genome ended in a virtual tie in June 2000, Celera began an abrupt decline in its fortunes, and in 2002, Venter was dismissed as its head. Venter subsequently switched his focus to philanthropic projects, and later that year founded The Center for the Advancement of Genomics (TCAG), a not-for-profit policy center in Rockville, Maryland. It studied social and ethical issues surrounding genomic science, including such issues such as genetic privacy, discrimination, and the genetics of ethnicity and stem cells. It was dedicated to education of the general public, elected officials, and students. TCAG published an online news magazine Genome News Network, whose publication continues to this day.
Also in 2002, Venter founded the Institute for Biological Energy Alternatives (IBEA) to research the possibility of using genomic techniques to engineer microbes with enhanced capacity to produce alternate fuels (such as hydrogen) as a clean energy source, as well as microorganisms engineered to sequester carbon dioxide. As part of its efforts, IBEA undertook large-scale genomic sequencing of environmental microbial populations hoping to discover new organisms that might be of value for its goals.
To provide production support for these facilities, Venter created the J. Craig Venter Institute Joint Technology Center (JTC), which specialized in high throughput sequencing: Under the leadership of Yu Hui Rogers, the JTC sequenced nearly 100 million base pairs of DNA per day for its affiliated institutions.
To provide administrative and financial support for TIGR, TCAG, IBEA and JTC, Venter created the non-profit J. Craig Venter Science Foundation (JCVSF). The TIGR Board of Trustees agreed to fund all these new ventures from the TIGR endowment, which became a joint endowment for all four entities. JCVSF coordinated policy and research activities between its affiliated organizations, and carried out investment management and fund-raising activities on their behalf. In addition, JCVSF explored ways to foster science education and scientific innovation.
2004 marked the beginning of a series of cost-cutting consolidations, beginning with the merging of TCAG, IBEA and JTC into the J. Craig Venter Institute (JCVI). The consolidations were complete by October 2006.
In 2011, the SCImago Research Group, based in Spain, ranked JCVI 6th worldwide on its Excellence Rate scale, and 10th on its Normalized Impact scale, taking into account "scientific impact, thematic specialization, output size and international collaboration networks". The JCVI website lists 2076 peer-reviewed publications from 1991 through early 2014, a large fraction of which emerged from TIGR during the years 1992-2006.
On its website, JCVI lists nine research/work groups:
- Genomic Medicine. The focus of this group is to provide an improved molecular understanding of human health and disease. A highly publicized accomplishment was their publication of the first diploid human genome, i.e. the genome of a single individual (J. Craig Venter) in which both sets of chromosomes were sequenced. Teams within this group are working on a protein-protein interaction map of E. coli, analyzing the genetic variants associated with disease as a step towards personalized medicine, and studying human microbial flora, both at the single-cell level and at the microbiome level as part of the Human Microbiome Project.
- Infectious Disease. This group is studying the three-dimensional structure of the proteins of pathogenic organisms, sequencing and genotyping organisms considered potential agents of bioterrorism, studying the mechanisms of microbial pathogenesis, studying viral genomics, and providing a centralized facility to the research community with resources to conduct genomics research on pathogens and disease vectors.
- Microbial & Environmental Genomics. This group is performing comparative genomic and proteomic surveys of Antarctic phytoplankton, sampling and cataloging life in the world's oceans, providing tools for the research community to access all of the publicly available bacterial genome sequences to date, and sequencing the genomes of hundreds of individual marine microbes.
- Plant Genomics. This group is studying the functions of plant genes, performing comparative genetic analysis, and tracking complex metabolic pathways, with particular attention to important food crops and industrial feedstock crops.
- Synthetic Biology & Bioenergy. This group is studying ways to engineer organisms to produce various kinds of biological products and renewable fuels. A highly publicized accomplishment was the complete assembly of a 1.08 million base pair Mycoplasma mycoides genome, which was then inserted into a cell to create the first cell with a completely synthetic genome.
- Policy Center. The mission of this group is to understand the implications of genomics science for society. This group aims to help decision makers understand and anticipate the impact of 21st century biology, the goal being to enhance positive and avoid negative outcomes of policy decisions.
- Informatics. This is one of the largest teams at JCVI, and includes software engineers and bioinformatics experts that develop and maintain the computational tools needed to study the vast amount of data generated by genomics methods.
- Sequencing. The high throughput sequencing activities are supported by the Informatics department and a technical team spanning multiple disciplines of biology, computer science and software engineering.
- Education. This group supports a variety of school and community educational initiatives.
- Comprehensive Microbial Resource
- Artificial cell
- The Institute for Genomic Research
- Global Ocean Sampling Expedition
- Mycoplasma laboratorium
- Shreeve, James (2004). The Genome War: How Craig Venter Tried to Capture the Code of Life and Save the World. Knopf. ISBN 0375406298.
- Sulston, John (2002). The Common Thread: A Story of Science, Politics, Ethics and the Human Genome. Joseph Henry Press. ISBN 0309084091.
- "The Human Genome Project Race". Center for Biomolecular Science & Engineering, UC Santa Claus. Retrieved 20 March 2012.
- Fleischmann, R. D.; Adams, M. D.; White, O.; Clayton, R. A.; Kirkness, E. F.; Kerlavage, A. R.; Bult, C. J.; Tomb, J. F.; Dougherty, B. A.; Merrick, J.; Al., E. (1995). "Whole-genome random sequencing and assembly of Haemophilus influenzae Rd". Science 269 (5223): 496–512. doi:10.1126/science.7542800. PMID 7542800.
- Pruitt, Kim D. (1998). "WebWise: Guide to The Institute for Genomic Research Web Site". Genome Research 8 (10): 1000–1004. Retrieved 20 March 2012.
- Pennisi, E. (1998). "HUMAN GENOME PROJECT:A Planned Boost for Genome Sequencing, but the Plan is in Flux". Science 281 (5374): 148–149. doi:10.1126/science.281.5374.148. PMID 9687268.
- Goozner, Merrill (19 December 2001). "Patenting Life". The American Prospect. Retrieved 20 March 2012.
- McElheny, Victor K. (2010). Drawing the Map of Life: Inside the Human Genome Project. Basic Books. ISBN 046504333X.
- Venter, J. Craig (2007). A Life Decoded: My Genome: My Life. Viking Adult. ISBN 0670063584.
- Rabinow, Paul; Dan-Cohen, Talia (2004). A Machine to Make a Future: Biotech Chronicles. Princeton University Press. ISBN 0691126143.
- Shreeve, James (August 2004). "Craig Venter's Epic Voyage to Redefine the Origin of the Species". Wired Magazine 12 (8). Retrieved 20 March 2012.
- Wade, Nicholas (27 June 2000). "Double Landmarks for Watson: Helix and Genome". The New York Times. Retrieved 20 March 2012.
- Fraser, C. M.; Gocayne, J. D.; White, O.; Adams, M. D.; Clayton, R. A.; Fleischmann, R. D.; Bult, C. J.; Kerlavage, A. R.; Sutton, G.; Kelley, J. M.; Fritchman, J. L.; Weidman, J. F.; Small, K. V.; Sandusky, M.; Fuhrmann, J.; Nguyen, D.; Utterback, T. R.; Saudek, D. M.; Phillips, C. A.; Merrick, J. M.; Tomb, J. -F.; Dougherty, B. A.; Bott, K. F.; Hu, P. -C.; Lucier, T. S.; Peterson, S. N.; Smith, H. O.; Hutchison Ca, 3.; Venter, J. C. (1995). "The minimal gene complement of Mycoplasma genitalium". Science 270 (5235): 397–403. doi:10.1126/science.270.5235.397. PMID 7569993.
- Bult, C. J.; White, O.; Olsen, G. J.; Zhou, L.; Fleischmann, R. D.; Sutton, G. G.; Blake, J. A.; Fitzgerald, L. M.; Clayton, R. A.; Gocayne, J. D.; Kerlavage, A. R.; Dougherty, B. A.; Tomb, J. -F.; Adams, M. D.; Reich, C. I.; Overbeek, R.; Kirkness, E. F.; Weinstock, K. G.; Merrick, J. M.; Glodek, A.; Scott, J. L.; Geoghagen, N. S. M.; Venter, J. F.; Fuhrmann, J. L.; Nguyen, D.; Utterback, T. R.; Kelley, J. M.; Peterson, J. D.; Sadow, P. W.; Hanna, M. C. (1996). "Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii". Science 273 (5278): 1058–1073. doi:10.1126/science.273.5278.1058. PMID 8688087.
- Fraser, C. M.; Casjens, S.; Huang, W. M.; Sutton, G. G.; Clayton, R.; Lathigra, R.; White, O.; Ketchum, K. A.; Dodson, R.; Hickey, E. K.; Gwinn, M.; Dougherty, B.; Tomb, J. F.; Fleischmann, R. D.; Richardson, D.; Peterson, J.; Kerlavage, A. R.; Quackenbush, J.; Salzberg, S.; Hanson, M.; Van Vugt, R.; Palmer, N.; Adams, M. D.; Gocayne, J.; Weidman, J.; Utterback, T.; Watthey, L.; McDonald, L.; Artiach, P.; Bowman, C. (1997). "Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi". Nature 390 (6660): 580–586. doi:10.1038/37551. PMID 9403685.
- Fraser, C. M.; Norris, S. J.; Weinstock, G. M.; White, O.; Sutton, G. G.; Dodson, R.; Gwinn, M.; Hickey, E. K.; Clayton, R.; Ketchum, K. A.; Sodergren, E.; Hardham, J. M.; McLeod, M. P.; Salzberg, S.; Peterson, J.; Khalak, H.; Richardson, D.; Howell, J. K.; Chidambaram, M.; Utterback, T.; McDonald, L.; Artiach, P.; Bowman, C.; Cotton, M. D.; Fujii, C.; Garland, S.; Hatch, B.; Horst, K.; Roberts, K.; Sandusky, M. (1998). "Complete genome sequence of Treponema pallidum, the syphilis spirochete". Science 281 (5375): 375–388. doi:10.1126/science.281.5375.375. PMID 9665876.
- White, O.; Eisen, J.; Heidelberg, J.; Hickey, E.; Peterson, J.; Dodson, R.; Haft, D.; Gwinn, M.; Nelson, W.; Richardson, D. L.; Moffat, K. S.; Qin, H.; Jiang, L.; Pamphile, W.; Crosby, M.; Shen, M.; Vamathevan, J. J.; Lam, P.; McDonald, L.; Utterback, T.; Zalewski, C.; Makarova, K. S.; Aravind, L.; Daly, M. J.; Minton, K. W.; Fleischmann, R. D.; Ketchum, K. A.; Nelson, K. E.; Salzberg, S.; Smith, H. O. (1999). "Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1". Science 286 (5444): 1571–1577. doi:10.1126/science.286.5444.1571. PMID 10567266.
- Read, T. D.; Salzberg, S.; Pop, M.; Shumway, M.; Umayam, L.; Jiang, L.; Holtzapple, E.; Busch, J.; Smith, K.; Schupp, J. M.; Solomon, D.; Keim, P.; Fraser, C. M. (2002). "Comparative Genome Sequencing for Discovery of Novel Polymorphisms in Bacillus anthracis". Science 296 (5575): 2028–2033. doi:10.1126/science.1071837. PMID 12004073.
- "Genome giant's next step". Prisma Techniek. Retrieved 20 March 2012.
- "Genome News Network". Retrieved 20 March 2012.
- Smith, HO; Friedman, R; Venter, JC (Summer 2003). "Biological Solutions to Renewable Energy". The Bridge 33 (2). Retrieved 20 March 2012.
- "Press Release: J. Craig Venter Announces Consolidation of Three Research Organizations Into One New Not-For-Profit Organization — The J.Craig Venter Institute". J. Craig Venter Institute. 29 September 2004. Retrieved 20 March 2012.
- "JCVI: About / Overview". J. Craig Venter Institute. Retrieved 20 March 2012.
- "SCImago Research Group". SCImago Research Group. Retrieved 21 March 2012.
- "JCVI: Publications / Listing". J. Craig Venter Institute. Retrieved 21 March 2012.
- "JCVI: Home". J. Craig Venter Institute. Retrieved 20 March 2012.
- Levy, S.; Sutton, G.; Ng, P. C.; Feuk, L.; Halpern, A. L.; Walenz, B. P.; Axelrod, N.; Huang, J.; Kirkness, E. F.; Denisov, G.; Lin, Y.; MacDonald, J. R.; Pang, A. W. C.; Shago, M.; Stockwell, T. B.; Tsiamouri, A.; Bafna, V.; Bansal, V.; Kravitz, S. A.; Busam, D. A.; Beeson, K. Y.; McIntosh, T. C.; Remington, K. A.; Abril, J. F.; Gill, J.; Borman, J.; Rogers, Y. H.; Frazier, M. E.; Scherer, S. W.; Strausberg, R. L. (2007). "The Diploid Genome Sequence of an Individual Human". PLoS Biology 5 (10): e254. doi:10.1371/journal.pbio.0050254. PMC 1964779. PMID 17803354.
- Gibson, D.; Glass, J.; Lartigue, C.; Noskov, V.; Chuang, R.; Algire, M.; Benders, G.; Montague, M.; Ma, L.; Moodie, M. M.; Merryman, C.; Vashee, S.; Krishnakumar, R.; Assad-Garcia, N.; Andrews-Pfannkoch, C.; Denisova, E. A.; Young, L.; Qi, Z. -Q.; Segall-Shapiro, T. H.; Calvey, C. H.; Parmar, P. P.; Hutchison Ca, C. A.; Smith, H. O.; Venter, J. C. (2010). "Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome". Science 329 (5987): 52–56. Bibcode:2010Sci...329...52G. doi:10.1126/science.1190719. PMID 20488990.