PALO ALTO, Calif.--The US National Institutes of Health have given Incyte Genomics a one-year contract to provide sequencing for one part of its Mammalian Gene Collection project. NIH is building a repository of full-length expressed human and mouse genes to be used in health and disease research. Gene sequence data and clones from this will be made available to the public. Incyte will confirm that the clones being selected are good candidates to provide full-length genes.
The gene project is being managed by the US National Cancer Institute and the US National Human Genome Research Institute and funded by most of the institutes at the NIH. Presently, only about 6,000 full-length gene sequences from the more than 100,000 suspected human genes are in the public domain.
Data and clones to be made public
All sequence data from this effort will be added to dbEST, a public repository for cDNA sequence data within GenBank. Clones will also be made available through the IMAGE (Integrated Molecular Analysis of Genomes and their Expression) Consortium, a group of academic institutions and private companies--including Incyte--that are placing genomic data and clones in the public domain.
Incyte was chosen in a competitive selection process, according to officials from NCI. Financial terms and names of organizations that competed with Incyte for the one-year contract were not disclosed.
Roy Whitfield, Incyte's CEO, said Incyte will provide library construction, sequencing, and bioinformatics under what he called its Custom Sequencing Service. Sequence information from the public project will be added to Incyte's LifeSeq database. He said the NIH project is consistent with Incyte's strategy to make genomic data available across the scientific community. Whitfield said Incyte will receive a "significant" amount of money from the deal, but he declined to specify.
"All our plans for development of databases are built assuming the public effort will do what it's doing. We want to embrace their efforts and integrate them into everything we're doing here at Incyte," Whitfield added.
Incyte a longtime public contributor
Incyte has been conducting sequencing for the Human Genome Project under contract to the University of Washington. That work, however, was not a factor in NIH's decision, said Jeffery Derge, head of research administration for Science Applications International of San Diego, Calif., a contractor that runs operations, technical support, and the computer center for NCI's Cancer Research and Development Center in Frederick, Md.
Need for speed
Incyte was selected because the project needed a high volume of sequencing done in a short period of time in order to "front-load the pipeline," said Derge.
"Very shortly, we're going to have several sequencing centers ready to go on several hundred full-length clones. We need to keep supplying them on a monthly basis with more and more clones as they go through the system," he explained.
NCI's pipeline is generating cDNA libraries from a variety of tissue sources, Derge explained. The initial step involves conducting a 5' expressed sequence tag sequence read on the clones. The US National Center for Biotechnology Information then carries out a bioinformatics test on the data and selects clones it deems likely to be full-length candidates, which will be arrayed again. Lawrence Berkeley National Laboratory is making the US Department of Energy's contribution to this project by arraying clones.
Incyte will perform a second EST sequence analysis to verify the clones that will be sent to laboratories chosen to carry out full-length sequencing. NIH has not yet completed negotiations with those labs.
Once a full-length clone has been verified using bioinformatics, it will be available as a research tool to any researcher through the IMAGE Consortium, said Derge. The consortium was founded in 1993 to accelerate gene discovery through the use of arrayed cDNA libraries, and to aid in the accumulation of sequence, map, and expression information for all genes. Both Lawrence Livermore and Lawrence Berkeley National Labs have been heavily involved in the consortium, added Derge. NCI has used IMAGE before as a distribution network for its Cancer Genome Anatomy Project.
It is difficult to say how long the project will take, said Derge, considering that the ultimate goal is to get a certified full-length clone of every expressed protein in humans. "That will not take place in one year," he said. It is expected that in the first few years, the project will be able to get the short- and medium-size clones relatively easily. The long ones, however, will be harder to get, he added.
When the announcement about Incyte's involvement in the mammal project was made, its stock price dropped as much as 11 percent. It was speculated that investors worried that collaborating with NIH might cut the value of Incyte's human gene database.