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Experts Say Analysis Is The Next Big Crunch The Genomics Community Faces


SAN FRANCISCO--A complex and demanding period of analysis and synthesis lies just ahead for the genomics community, according to speakers who addressed 450 attendees at In Silico Biology and the 8th Bioinformatics and Genome Research Conferences, two meetings held here June 8-10 and 14-15 by Cambridge Healthtech Institute. The group also hosted a Proteomics conference June 9-11.

Commenting on how improved equipment has accelerated progress, Gene Myers, director of informatics research at Celera Genomics, said, "the advent of the Perkin-Elmer ABI Prism 3700 capillary gel sequencing machines made massively scaled-up shotgun assembly feasible. False reads went down and the lane-tracking problem went away." He added, "Analysis, not assembly, is the big crunch today."

Frank McCormick, director of the University of California San Francisco Cancer Center, noted how far science has come during the pregenome era in codifying pathways such as Ras, Rb, and p53, and identifying mutations that result in gain and loss of gene function. "Twenty years of pregenomics biology have given us the pathways and the potential targets," he said.

The next wave of research will be to compile complex patterns of cancer genomes, with their deranged regulation, copy number, and transcription rate. "At this point we can only see it in a simplistic, reductionist way, but bioinformatics will fill it in and amplify it," McCormick predicted.

Adam Arkin, of the Lawrence Berkeley Laboratory, said biological systems now being revealed require a synergistic approach. "We have full knowledge of the parts list and the individual instructions, but it's so large and complex that we can't holistically grasp it all," he said.

John Weinstein, senior investigator in the Laboratory of Molecular Pharmacology at the US National Cancer Institute, stressed that the current revolution in drug discovery hinges as much on a change in viewpoint as on technology. Traditional one-gene-at-a-time academic research tends to be "hypothesis-bound rather than data-driven," as biological discovery must become in the future, he asserted.

Considering the current rate of expansion of biological information, Thure Etzold, vice-president of bioinformatics research at Lion Bioscience in Heidelberg, compared the era to the Big Bang, with information hurtling outward from a central event and each database representing a galaxy of information.

Chris Overton, director of the Center for Bioinformatics at the University of Pennsylvania, commented, "We're only at the dot-matrix stage of database integration today, and already there are problems." In the future, scientists will be faced with the need for incorporating phenotype and patient information in working datasets, posing acute challenges to existing methods of information handling.

--Potter Wickware

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