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Genome Annotation Report: Need new annotation initiative, funding options


Rich Roberts has an unusual beef with genomics funding agencies: there’s no way to get less money out of them. Roberts, a research director at New England Biolabs who focuses on the biochemistry and bioinformatics of restriction enzymes and DNA methyl transferases, argues that efforts in genome annotation haven’t produced as much data as they could have, and that one reason is the lack of a funding mechanism for small-scale projects.

In a report Roberts coauthored through the American Society for Microbiology, he puts forward an idea for a high-throughput genome annotation initiative that would begin with prokaryote genomes and entail the establishment of a central genome annotation database. Prokaryotic organisms are ideal because “the genes are not split into pieces” and “the genomes are smaller and more manageable,” Roberts says. Besides, progress with a prokaryote is a first step toward much more complex organisms, he adds. “If we’re ever going to understand how life works, we’ve got to understand how the simplest life works.”

Roberts had stumbled upon a very simple idea to get the annotation community moving forward: using the work done by a lab’s rotation students to fill in holes in genome knowledge. “It’s a good project for a graduate student,” he says. “[They can] clone out the gene and make a protein test for activity. … If they were lucky they could actually identify the biochemical function and they could get a paper out of it. If the lab were given a little bit of money as a reward for having done it, there would be incentive for them to put students on this.”

Roberts isn’t exaggerating when he says “little amount” — he’s talking $5,000, maybe $10,000 to cover this kind of work. “If you’ve already got a rotation student to do the work and you already have the substrates and the expertise in your lab, then the incremental costs are actually quite low.” Even a $5,000 grant would more than cover expenses and still provide some incentive, he says.

In the report, authors suggest gathering a core group of bioinformatics experts to identify good candidate genes for students to work on. That master list would be posted online, and people from labs around the world could sign up to do one or two. “It’s a high-throughput project — in parallel rather than in series,” Roberts says.

Roberts originally published this concept in a paper in PLoS Biology, and when he forwarded it around to some people at funding agencies, they took note, inviting him to convene a workshop to talk about this issue. Roberts says the idea was well received at the workshop, but that creating a new funding mechanism will be a major cultural challenge for the agencies.

Still, he argues, pursuing genome annotation is a sensible step in the progression of dollars spent on genomics. “Funding agencies are spending a huge amount of money on genome sequencing,” Roberts says, “and the only way you’re going to get the value back out of that is” by thoroughly annotating that sequence.

— Meredith Salisbury


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