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Functional Genomics With $12m, NHGRI Launches Genome Analysis Project


Just when you thought the human genome would have a chance to relax for a while, NHGRI is stirring things up again. This time, it’s a project called ENCODE — the Encyclopedia of DNA Elements — and $12 million is up for grabs to draw researchers in.

“This is something we’ve been thinking about for a while in terms of how are we really going to figure out what is in the genome when we have a complete sequence,” says Elise Feingold, NHGRI program director and lead person for ENCODE. The solution is a pilot project to aggressively study one percent of the human genome with the best available tools and techniques to see which technologies work and where the gaps are in scientists’ ability to determine all the functional elements of the genome, Feingold says.

“We’re pretty good at finding the genes and transcription elements, but we’re not even able to do that to 100 percent accuracy,” she adds. “Beyond that … the path to identify all of those [other] elements is really not clear.”

The project, which kicked off last month, will include a consortium of researchers — NHGRI is hoping to see participants from both the public and private sectors — who will be responsible for in-depth study of the genome.

They’ll be looking at one percent, or 30 MB, of human genomic sequence, in regions ranging from about half a megabase to 2 MB. The regions were chosen both manually, based on sequence that already has considerable information associated with it, and automatically, through a process that stratified the genome by GC content, for one, and then chose randomly to get a “good cross-section of different types of sequence,” Feingold says.

The selected sequence will encourage work that gets past the usual suspects: genes, coding sequences, promoter regions. Every member of the consortium will be looking at the whole shebang: “We don’t want people coming in and working on their favorite region,” she says. “Whoever’s participating needs to agree to work on the entire set of targets.” Participants must also agree to NHGRI’s data-release policies.

As the consortium gears up, a second component will start as well. Grants have been set aside for simultaneous tech research because “we recognize that there are probably a lot of additional technologies that need to be developed,” Feingold says.

Several years from now, the information gleaned from the consortium will be combined with the new technologies for phase three: what she expects will be “a much more complete understanding of the human genome.”

The consortium’s work will be funded by $10 million in grants (although Feingold emphasizes that anyone can take part, whether they’re funded by this RFA or not). Grant size hasn’t been capped, and Feingold expects to see a “wide range” in the amounts awarded. Technology development has $2 million in separate grants, which have been capped at $350,000 per year. Applications are due May 13. “We always encourage people who are interested in applying to contact us before they submit their application,” Feingold says. She hopes to have funding in place for grant awardees by the end of September.

— Meredith Salisbury


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