Influential Consortium's cDNA Clones Praised As Genome Research Time-Saver

IMAGE group's DNA libraries are made freely available to other researchers, as long as they, too, pass on information to the public. In less than two years, a research initiative begun by four geneticists has grown from an ad hoc collaboration to an international cooperative effort to freely share complementary DNA (cDNA) clone libraries. To date, in excess of 100,000 clones from the Integrated Molecular Analysis of Genome Expression (IMAGE) Consortium have been sent to more than 40 facilities worldwide. Scientists describe the consortium's informal approach to genetic information sharing as "refreshing," especially in light of recent debates over intellectual property rights derived from genome research. More important, they say, the widespread disbursement of IMAGE cDNA clones decreases the time it takes investigators to extract information from the human genetic code, thus greatly facilitating the hunt for new genes and, ultimately, new drugs. IMAGE INITIATORS: Consortium cofounders, from left, Bento Soares, Mihaelis Polymeropoulos, Charles Auffray, and Greg Lennon. "I think it's clear that the ability to work with a common set of resources--be it a cDNA or another type of library--makes life easier for researchers tackling the enormous task of characterizing the human genome," observes Francis Collins, director of the National Center for Human Genome Research (NCHGR). "As people do sequencing, [IMAGE clones] will provide many landmarks" on the vast genetic map, notes David A. Smith, director of the health effects and life science research division of the Department of Energy (DOE). The consortium--initiated in November 1993 by Greg Lennon, a senior scientist at DOE's Lawrence Livermore National Laboratory (LLNL); Charles Auffray, a scientist with CNRS in Villejuif, France; Bento Soares, an assistant professor of neurogenetics at Columbia University; and Mihaelis Polymeropoulos, a researcher with NCHGR--was essentially born out of necessity. "A group of us were sitting around [at a meeting] bemoaning the fact that every [genome research] group seemed to work with their own set of clones," Lennon recalls. "We initially saw ourselves as a pipeline where Bento would produce the cDNA libraries, I would array and track all of the information, Charles would sequence, and Mihaelis map." But that pipeline has grown into a global network of direct and indirect users of the clones or the sequencing and potential genome-mapping information they contain. For instance, IMAGE clones are being used in a Merck & Co. Inc.- Washington University sequencing project, which got under way in January (F. Hoke, The Scientist, Dec. 12, 1994, page 1). "The overall goal [of IMAGE] is to facilitate genome characterization in the most efficient way," Lennon explains. "Primarily, this is done by coordinating cDNA resources such that information derived from these publicly available, royalty-free clones--be it sequence, map, or expression data-- can readily be integrated, regardless of who does the work, where it is carried out, or what database it winds up in." For now, there's no direct funding for the consortium's efforts. The four founders initially established IMAGE to facilitate their primary research projects. As IMAGE has grown, so has the time spent distributing and maintaining the clones, says Lennon. As a result, the consortium is in the process of identifying commercial distributors, who would charge a nominal fee for shipping and handling. GENETIC MILE MILEPOSTS: "As people do sequencing, [IMAGE clones] will provide many landmarks," according to DOE's David A. Smith Guidelines for obtaining an IMAGE clone stipulate that recipients may use a clone for any purpose as long as they submit any sequence, map, and expression data they develop from it to an appropriate public database. Users also agree to not disclose or transfer data to any outside commercial enterprises until the genetic information is in a database. Clones cannot be sold, but can be passed on for free to anyone as long as that person also agrees to IMAGE's stipulations. At the same time, there are no creative restrictions on using the clones: Any inventions belong solely to the inventing party. General information on IMAGE is available via E-mail at info@image.llnl.gov. This address provides answers to frequently asked questions and other addresses for more details on how to obtain clones. The IMAGE E-mail helpline is: help@image.llnl.gov. IMAGE is also available through the World Wide Web at: http://www-bio.llnl.gov/bbrp/genome/genome.html. The dbEST database, which includes expressed-sequence tags of IMAGE cDNA clones, can be accessed via the National Center for Biotechnology Information's WWW server: http://www.ncbi.nlm.nih.gov/ For general information on dbEST, send E-mail to: info@ncbi@nlm.nih.gov; or call (301) 496-2475 and ask for the service desk. dbEST is also linked to other databases, such as the European Bioinformatics Institute near Cambridge, England, via the WWW server: http://www.ebi.ac.uk/ --K.Y.K. Lennon acknowledges that there is a philosophical subtext running through these requirements: "We want people to know that our clones are freely available and that the genome as a whole shouldn't be patentable." Merck's Alan Williamson, vice president of research strategy worldwide, and Keith O. Elliston, associate director for bioinformatics, took a similar stance in a letter to Nature (372:10, 1994). "Together, we [IMAGE and Merck] agree that [genetic] information should not be the subject of exclusive ownership, nor should the clones on which it is based," adds Lennon. He compares the relationship of gene discovery and ownership to the naming of species by the Swedish botanist Carl Linnaeus in the 18th century: "It's our belief that merely naming a gene or being the first to come across a piece of the world that was unknown--just as Linnaeus came across an unknown species and gave it a name--should not confer exclusive ownership to that gene or species. That's not a correct basis for intellectual property rights." The bulk of IMAGE's clone resources are based on Soares's normalized cDNA libraries--collections in which the number of multicopy cDNAs are reduced so that rare cDNA types can be more easily found. The cDNA clones represent DNA copies of messenger RNA (mRNA) joined to a cloning vector, allowing for propagation in bacteria. Because cDNA strands represent expressed--that is, encoding for one of the estimated 50,000 to 100,000 genes found in humans--portions of the genome, they are thought to identify its most biologically and medically significant information. The four Soares libraries donated so far are derived from infant brain, liver and spleen, placenta, and breast tissues and are believed to represent 20,000 to 40,000 different clones. Many investigators maintain that his "green thumb" for preparing these libraries is one reason for IMAGE's good reputation among genome researchers. Collins also appreciates Soares and Columbia's decision to make the libraries publicly available instead of retaining exclusive patent rights to them, although Columbia does retain the right to license other, unnormalized libraries created by Soares and has a patent pending on his normalization technique. >From the libraries provided by Soares and other laboratories, Lennon creates arrayed cDNA libraries. These are cDNA collections in which a bacteria colony carrying one type of clone lives in each thimble-sized well of a 384-well microtiter plate. Each clone is given an identifying number so that it can be matched to its nucleotide sequence and map information in genomic databases. "Arrayed cDNA libraries enable researchers anywhere in the world to work more efficiently," says Lennon. He cites two technological breakthroughs that set the stage for IMAGE: "The first one is the concept of arraying," which has been collectively developed by many researchers using genomic clones, notably Hans Lehrach while at the Imperial Cancer Research Fund in London. "The second part of this is the cDNA sequence tag approach exemplified by a number of investigators, including J. Craig Venter [president of The Institute for Genomic Research (TIGR), a nonprofit facility in Gaithersburg, Md]." These tags--commonly called expressed- sequence tags, or ESTs--represent partial sequences of cDNA, which nonetheless are specific enough to use in subsequent sequencing or mapping research. IMAGE expects to have the first in a series of human cDNA master arrays available later this year. "The concept of a master array is to pick from our whole collection one clone representing each gene so that, ultimately, we will represent the greatest number of genes with the fewest clones," thus saving researchers even more work. IMAGE also has plans to do similar types of arraying with non-human cDNAs. Initially, Auffray sequenced all the IMAGE clones, and has deposited more than 25,000 sequences and 2,000 chromosomal assignments into public databases; other scientists have sequenced IMAGE clones, as well. But the use of IMAGE clones really grew when, last October, Merck announced its project to develop a complete set of publicly available human cDNA sequences. "The idea [for Merck's project] started in May 1994," recalls Williamson. "Then we discovered last summer that IMAGE was coming together." In the meantime, Merck chose the Washington University (WU) Genome Sequencing Center to perform the sequencing. IMAGE agreed to lend its arrayed cDNA libraries to the WU-Merck endeavor. All sequences from that project are derived from IMAGE clones. "Sequencing actually started in January," says Richard K. Wilson, research associate professor of genetics and co- principal investigator at WU's genome center. "It'll run at its current capacity [of roughly 4,500 clones per week] through the end of the summer. Then, in the last six months, we'll concentrate on clones we haven't sequenced before. The whole thing from start to finish will run 18 months." Sequences produced by WU are submitted daily directly into dbEST, an EST database that is a division of GenBank, the public super-database managed by NIH's National Center for Biotechnology Information (NCBI) in Bethesda, Md. Other contributors to dbEST include TIGR, which has donated more than 10,000 sequences. "We processed 113,827 sequences as of April 15; 69,400 of those were submitted to dbEST," says WU's Wilson. Mark Boguski, senior scientist at NCBI, reports that "dbEST usage has steadily increased since it went online three years ago, but usage increased exponentially once the [IMAGE] data started appearing. "Homology searching and E-mail retrieval doubled in the first quarter of 1995 compared with the fourth quarter of 1994. But the most dramatic increases have come from World Wide Web accesses and ftp file transfers, which have increased four- and ten-fold, respectively, over the past six months." NEXT STEPS: There are plans to map a large number of gene sequences derived from IMAGE clones, reports Hopkins' genome database director, David T. Kingsbury David T. Kingsbury, director of the Genome Database at the Johns Hopkins University School of Medicine, says that it "is too soon to say" how many genes are represented by the IMAGE clones, but "there are plans to map a large number of them." As a cofounder, Polymeropoulos was the first genetic mapper aligned with IMAGE, "primarily mapping polymorphic cDNAs, especially those containing di- or tri-nucleotide repeats," according to Lennon. But now many researchers are involved in mapping projects using information derived from IMAGE clones. Kingsbury notes that Wellcome Trust in England has tentatively committed funds to do some of this, and in the United States "there's some discussion to map arrayed cDNA libraries against other types of gene libraries." For now, as cDNA clones donated to IMAGE are arrayed, their sequences are entered into the Hopkins mapping database. With special codes, mapping information can be linked back to dbEST and the original arrayed clones. Basic scientists also use IMAGE clones in their studies of proteins. Yale University cell biologist Ira Mellman has received IMAGE clones to aid in studying a widely expressed protein involved in intracellular protein sorting. He and others will express the cDNA clones to explore the possible cellular function of the protein. He says having access to the original clones saves an "enormous amount of time, effort, and money to find out whether the cDNAs are really interesting" biologically, which can't be fully determined from their sequences alone. "You can go directly from a hunch that you have [about a protein] into going about the business of researching its cell biology."

Influential Consortium's cDNA Clones Praised As Genome Research Time-Saver

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