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FEATURE: Researchers Meet to Set Criteria for Sequencing Genomes

WASHINGTON, DC, July 10 – Rather than “greasing the squeakiest wheel,” a broad panel of biologists met July 9 and 10 in Washington, DC, to find more equitable ways to decide which genomes should be sequenced next.

The workshop, called Developing Guidelines for Choosing New Genomic Sequencing Targets, was not meant to decide which specific genomes should receive top priority. However, the participants agreed on several criteria, namely, that the genome should be of manageable size, useful to a large number of researchers, relevant to human health, and that researchers should be able to experiment with the organism. In addition, the scientists said an organism located at a key branch point on the evolutionary tree would also take prioity.

The workshop, co-chaired by Bob Horvitz, a biologist at the Massachusetts Institute of Technology, and David Botstein, a geneticist at Stanford University, attempted to bring together biologists from outside the immediate sequencing community and provide a forum for the researchers to present their views on how to make funding decisions. 

"We're looking for wise advice on how we might take the considerable resources that now exist for large-scale sequencing and deploy them for maximum advantage," said Francis Collins, director of the National Human Genome Research Institute (NHGRI) at NIH, whose agency sponsored the workshop and controls much of the money for genome sequencing.

"I'd like us to think of this as a guide to proposers," Botstein said, adding that researchers with proposals, reviewers, and the NIH administration should all be using the same general priority guidelines and then work out the details in the proposals. "When we've tried to specify too much from the center, that's when we've gotten into trouble," said Botstein.

An important question to ask, Horvitz added, is how a particular discipline would make use of sequence data from a particular organism. In some cases, a whole genome sequence is necessary, in others, partial sequences may be sufficient.

Eric Green, the director of intramural sequencing at NIH and NHGRI researcher, spoke to the workshop about his research into this question. His project, an effort that has been underway for about nine months, aims to compare the sequences of targeted regions in multiple vertebrates. Green’s team is initially examining two regions in the genomes of human, chimpanzee, baboon, cat, dog, cow, pig, rat, mouse, chicken, zebrafish, and fugu. Green said that over the next year the project will produce about 125 Mb of shotgun sequence, with about a third of this in finished form. 

Such analysis is essential to deciding how to distribute resources, as funding organizations decide whether they can afford to sequence both the chimpanzee and the gorilla, as evolutionary biologists would like. In addition, researchers must decide if sequencing longer genomes, such as the salamander genome, are worth the extra cost. 

One thing everyone is agreed on is the desirability of getting more for the available money. "We need to continue ramping down sequencing costs," said Bill Gelbart, a cellular biologist at Harvard University, "so that more can be done."

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