Volume 17 Number 3 FALL 2000

a new mission for the genome technology center

With DNA sequencing work nearly finished, the center's staff focuses on discovering genes' functions.

IT'S GOT A NEW NAME TO GO WITH ITS NEW AIM: THE STANFORD DNA SEQUENCING AND TECHNOLOGY CENTER IS NOW THE STANFORD GENOME TECHNOLOGY CENTER. "DNA sequencing" is gone from its name because the center's sequencing work is largely done. The major research question these days at the center: What do all these genes actually do?

To celebrate the completion of several large-scale sequencing projects and to stimulate new research collaborations and technology transfer, the center hosted an open house in June. The event brought together about 700 people, including scientists and engineers from academia and industry, to mingle over snacks and high-tech sequencing machines.

The event's success brought welcome attention to the center, which is located off campus on Palo Alto's California Avenue -- well off the beaten path for most of the campus community. "We've realized that many people don't know that we exist," says biochemistry professor Ron Davis, the director of the center. "This may be partly because we don't have a building on campus, and partly because we've been very busy doing a big job."

The big job has included sequencing portions of the fungus Candida albicans and participating in an international effort to sequence the genome of the plant Arabidopsis thaliana. Along the way, center staff members, which include biologists, engineers and software designers, have designed and built some of the most sophisticated robotic sequencing machines around. The new technology has enabled faster, more efficient DNA sequencing, with an error rate of only about one base per 10,000 bases.

Indeed, the technology on display would make nearly any biomedical science graduate student drool. Robotic plasmid prep machines have the capacity to isolate more than 1,100 of the small circles of DNA from bacterial cultures in only 12 hours. Automated sequencing machines can crack the nucleotide code of more than 300 samples in the same time period. Now the center is ready to apply this technology to the relatively new field of functional genomics, which endeavors to discover genes' functions.

"The sequence itself is an achievement, but figuring out what it all means is what will go on for years and years," says Nancy Federspiel, PhD, head of the Arabidopsis project. Researchers at the center have been working for four years to sequence a portion of the plant's chromosome 1. The entire genome sequencing is expected to be completed by the end of the year. Its completion will mark the first time that a plant genome has been entirely decoded.

"It's really cool to have a representative genome from another kingdom," says Federspiel. Although Arabidopsis is used mainly for scientific study, similarity between plant genomes means that the completion of the Arabidopsis sequence may have important implications for agriculture, she says.

Federspiel, an associate director of the center, also headed the effort to sequence a portion of the genome of the fungus Candida. Candida usually causes only mild infections in healthy people, but it can be very dangerous to immunocompromised individuals, such as HIV-infected people or transplant patients receiving immunosuppressive drugs. According to Federspiel, analysis of the sequences of both strands of Candida may identify particular genes that are responsible for the increased pathogenicity of certain strains and pinpoint weaknesses in the fungal life cycle that may be susceptible to new antifungal drugs.

The NIH's National Human Genome Research Institute has funded the center since 1993. For more information about the Genome Technology Center's ongoing projects, visit www-sequence.stanford.edu. -- KRISTA CONGER