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JGI Outlines Bioinformatics Needs at Human Genome Meeting

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SANTA FE, NM--The US Department of Energy (DOE) Joint Genome Institute hopes to double gene sequencing speed over the next two years and share the faster technologies with industry and academic researchers, DOE officials told the Sixth Annual DOE Human Genome Program Contractor and Grantee Workshop. The meeting was held here November 9-13.

So far, researchers have sequenced 60 million--or 2 percent--of the estimated 3 billion base pairs found in the human genome, according to DOE biologist Dan Drell. But they will need quicker, more powerful bioinformatics tools if they are to meet a September 30, 2005, deadline for finishing the job, noted Tom Slezak, the institute's team leader for informatics. "We will need more processing power every year," he said. One way Slezak's team, which is based at the Lawrence Livermore National Laboratory, hopes to accelerate the process is by automating sample preparation and increasing the power of finishing sequence processors. His team is also in the process of scaling up shotgun and transposon-based sequencing. Such techniques should allow the institute to double its sequencing speed from 20 million base pairs next fiscal year to 40 million in 1999. Within five years, sequencing improvements should allow institute scientists to process 100 million-200 million base pairs a year, he said.

Other kinds of help could come from a new generation of sophisticated bioinformatics tools, a number of which were displayed at the workshop. Slezak was particularly impressed with the Genome Channel web tool developed at the Oak Ridge National Laboratory. The tool--demonstrated by Ed Uberbacher, head of the Annotation Consortium--allows researchers to analyze genes on the web.

Drell noted that informatics researchers have made great strides in recent years, but still face a number of complex problems. For example, he noted that 3-D image technology needs to improve so that after researchers identify genes, they can then predict how the polypeptides encoded by the gene fold interact with other molecules. So far, Drell said, bioinformatics can help researchers predict "where a gene may be, but not what it does."

In addition to bioinformatics tools and techniques, the 370 people attending the workshop discussed the ethical, legal, and social ramifications of genomic research. They also heard about the institute's plans to build a facility at Walnut Creek, Calif., that should be operational by next summer.

Officials said the institute--a joint effort by DOE's Los Alamos, Lawrence Berkeley, and Lawrence Livermore national laboratories--has not yet decided how to staff the facility.

--Joe D'Allegra

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