The US National Cancer Institute this week said that it will provide $35 million over three years to support as many as four Cancer Genome Characterization Centers. Approximately $11.7 million will be allotted this year, according to the NCI's request for applications.
The centers, part of the Cancer Genome Atlas project, should be a major source of public cancer data that may provide the basis for future targeted cancer drugs, diagnostics, and combination products.
Additionally, the Atlas and its smaller components, such as the CGCCs, should drive the development of technologies for investigating cancer, which would benefit genomic tools companies, molecular diagnostics firms, and drug developers, as well as disease researchers.
"I think that molecular diagnostics and this whole issue of technology development are going to be critical to the ultimate success of this [Atlas] project," Anna Barker, deputy director of advanced technology and strategies at the NCI, told Pharmacogenomics Reporter this week.
A separate RFA related to the cancer atlas project will also be issued as early as June to support new technology development. The NCI has not yet determined the grant's size, but the grant aims to improve molecular characterization methods, such as gene expression, DNA sequencing, and epigenomic analysis, as well as methods of correlating disease states with genomics, according to an NCI spokesperson.
"I think both the biotech and the pharma industry will benefit enormously from this project — this is the way to get a set of data out there, from which you can find new targets."
Data from the CGCCs will go straight to a public database after some processing for quality assurance "so that people actually get useable data," Barker said.
The CGCCs will produce data and develop bioinformatics tools to help select candidate genes and genomic regions for sequencing by separately funded Genome Sequencing Centers associated with the project. "They're going to be driven much more by understanding the biology and bringing that knowledge base to the genome characterization and the clinical data, aggregating that into a database, and then using that as a group to identify new targets," said Barker.
Barker and colleagues have had some discussion about whether the CGCCs will focus on growth-factor receptors and other targets relevant to pharmacogenomics, she said.
"We obviously will start with … those things we know about, in terms of their importance in the carcinogenesis process, but I don't think we want to come to this with a lot of preconceived notions about what might be discovered here," she added.
The project will begin by looking at "known and suspected targets," Barker said.
Many pharmaceutical companies are doing very similar target characterization in-house, albeit on a smaller scale. "I think both the biotech and the pharma industry will benefit enormously from this project — this is the way to get a set of data out there, from which you can find new targets," said Barker.
A centralized Human Cancer Biospecimen Core Resource will supply the CGCCs with biomolecules from "highly annotated, quality-controlled human cancer" samples, according to the RFA.
The samples will include DNA, RNA, and maybe protein, although the method of characterization and which samples will be studied by each CGCC will be up to the discretion of applicants. "They're going to tell us," Barker said. "Some of the more complex centers will probably be doing all three."
Asked whether the CGCCs will incorporate technologies or methods important to pharmacogenomics, Barker left it to the applicants to decide. "We're hopeful that those perspectives will hopefully drive some original thinking in that regard. … I think there are a lot of smart people out there who will, I believe, approach this from different ways, and I believe that will be one of them," she said.
The CGCCs will probably set up shop at academic centers, with the functions of each either housed under a single roof, or split between several members, depending on applicants' qualifications, said Barker. "We expect that a lot of these academic centers are going to partner [with] folks in the private sector," she added. "We're curious to see how creatively these folks put these [applications] together."
Each CGCC is tied to the project through a management structure and each has throughput requirements of 1,000 samples per year after the first six months. By the second and third years of the project, the CGCCs should be exceeding that rate, according to the RFA.
"I think that molecular diagnostics and this whole issue of technology development are going to be critical to the ultimate success of this [Atlas] project."
"The technologies utilized by the CGCCs should maximize genome coverage and resolution to provide, to the greatest extent possible, a complete set of information on the cancer genome, epigenome, [and the] transcriptome," the RFA said.
In order to realize that acceleration in sample analysis, the NCI expects innovators to bring to the cancer project new methods and devices as it progresses, in a fashion similar to that of the Human Genome Sequencing project, said Barker.
"We're going to depend on technology innovation and maturation to really bring the cost down of what we're trying to do, as well as to provide the diagnostic technology to support things like targeted drug development," she said.
The next RFA associated with the Atlas may be issued as early as June. "It's not a lot of money, but it'll be enough to get some of the smaller companies potentially engaged through their academic collaborators," said Barker. "And there's a big SBIR piece of this as well."
The first true medical sequencing endeavor, the Cancer Genome Atlas is a pilot effort that, if successful, will be followed by a larger cancer genome-sequencing project. Even so, there is an enormous amount of data to be gathered and interpreted, due to the number of different types of cancer cells that the Atlas aims to study.
The pilot project will focus on two or three tumor types, and it will "extensively" characterize the genomic state of hundreds of tumors of each of these types, Francis Collins, director of the US National Human Genome Research Institute, said during a December interview.
The three-year Atlas itself is funded by $100 million from the NCI and the NHGRI, which are each contributing half of the cost.
Asked whether funding for the CGCCs would be supplemented after the project's three-year run, Barker said, "The current budget environment doesn't allow me to say that there will be any more money for anything — it's just a terribly difficult time right now." The CGCCs should also be able to attract funds from private sources, such as foundations interested in cancer-related research, she added.
— Chris Womack ([email protected])