NEW YORK (GenomeWeb News) — The National Human Genome Research Institute is expected not to renew funding for large-scale sequencing centers at Agencourt Bioscience and the J. Craig Venter Institute’s Institute for Genomic Research/Joint Technology Center, GenomeWeb News has learned.
The disclosure, made by an official and a senior scientist at the two centers who were briefed internally on the funding decisions, comes less than two weeks before the NHGRI announces how it will dole out $420 million over the next four years to large-scale sequencing centers, including labs at Baylor College of Medicine, the Broad Institute of MIT and Harvard, and Washington University School of Medicine.
It is likely that these three centers will split the $420 million among themselves.
An NHGRI spokesman declined to comment, saying that the institute will reveal details of the awards in mid-November. Senior officials at the five centers declined to comment for the same reason, or did not return repeated requests for comment.
If the NHGRI’s decision to consolidate the number of centers in this latest round holds, it will not be a surprise. Agencourt’s center and the TIGR/JTC facility received significantly less NHGRI funding than the other three centers during the last round, which started in late 2003: Over fiscal years 2004-2006, Agencourt received $28.88 million, the Venter Institute $29.02 million, Baylor $92.25 million, Washington University $130.75 million, and the Broad Institute $167.22 million, according to NIH databases. These figures include supplemental funding in fiscal years 2004 and 2006.
However, Agencourt and the Venter Institute may have cash left over from their previous grant: Funding granted in fiscal 2006 for Agencourt expires in October 2007, and for the Venter Institute in August 2007, while the same funding for the other centers runs out this fall.
For Agencourt and the Venter Institute this constitutes an “extension of funds,” the NHGRI spokesman told GenomeWeb News. It was unclear, though, whether this means the centers can use their existing funding in 2007, or whether they will obtain additional funding under the old grant next year.
Doling Out Change
According to the NHGRI’s request for applications for the new funding round, the institute plans to award a total of up to $420 million to three to five centers over four years. In the first year, the institute expects to spend up to $130 million. The earliest anticipated start date of the program was Nov. 1.
The NHGRI spent around $448 million in large-scale sequencing grants over the past three years. Like in previous years, this year’s sequencing program seeks to fund centers that “maintain and extend the state of the art for high throughput, low cost genome sequence data,” according to the RFA.
However, the nature of the sequencing projects is also likely to change in the next few years, especially as new sequencing technologies enter the centers.
“In addition to generating sequence data using Sanger-based sequencing technology for the purpose of assembling whole genome sequences, sequence data produced by other technologies and applied to different purposes are becoming even more important to biomedical research,” the institute said in the RFA. Accordingly, NHGRI plans to choose centers “that are capable of producing sequence data for projects other than whole genome sequencing.” It also “intends to provide adequate funding” for the centers to adopt new technologies.
Over the next four years, the institute said it expects improvements in existing instruments and the adoption of new technologies to lower sequencing cost at least five-fold. As a result, “projects once seen as important but too expensive will become reasonable, and entirely new kinds of highly significant projects will become possible,” according to the RFA.
Thus, the targets the sequencing centers will tackle in the future “will increasingly be based on large, compelling scientific questions and less on identifying individual organisms.”
Specifically, NHGRI sees opportunities in medical sequencing, cancer genome sequencing, human genotyping, comparative genome sequencing, parasite and vector genomes, and model systems. However, it acknowledges that other areas may be added since “new opportunities for the use of genomic sequence are not always predictable but continue to arise with some regularity.”
For cancer genome sequencing, the institute has committed $16.7 million per year in fiscal years 2007-2009 for the Cancer Genome Atlas (TCGA), a collaboration between NHGRI and the National Cancer Institute. The large-scale sequencing centers “will have the opportunity to participate in this program,” according to the RFA.
In addition to embarking on new kinds of sequencing projects, the centers must also be able to produce a “variety of types of sequence data beyond whole genome shotgun,” the institute specified, for example “directed sequencing reads for medical sequencing projects, EST or SAGE tag sequencing to aid annotating genome sequences, finished sequence data, improved or refined draft genome sequences.”
Finally, the new sequencing centers will have some control over how to spend their funding: Though the National Advisory Council for Human Genome Research will continue to select most of the sequencing targets, the centers will be able to devote up to 10 percent of their capacity to targets of their choice.
Julia Karow covers the next-generation genome-sequencing market for GenomeWeb News. E-mail her at [email protected]