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FEATURE: Will Fewer Genes Help Comparative Genomics Efforts?

NEW YORK, Feb 14 - For some companies -- namely those attempting to sell tools and databases claiming to have 60,000 to 120,000 human genes -- Monday's news that the genome may contain far fewer genes than previously expected may have sounded a bit harsh to the ears. 

But for others, the findings were cause for celebration.

Companies selling comparative genomics services say that having fewer genes in the human genome could make the task of deciphering gene function more manageable, and that the high degree of similarity across animal species demonstrates the value of studies using comparative techniques.

"The smaller size [fewer genes] is a validation of our approach," said Glen Sato, chief financial officer at Exelixis, a South San Francisco-based seller of comparative genomics data using nematode and drosophila models.

Fewer uniquely human genes, a finding supported by Celera's data showing that humans have only about 300 genes not found in mice, should allow comparative studies using other, simpler organisms to identify the function of human genes more accurately, explained Sato.

Other companies in comparative genomics voiced similar optimism. Brian Zambrowicz, senior vice president of genomics at Lexicon, said that "the lower number of genes means the function of each gene has more significant value. With 30,000 genes, suddenly the project [of determining gene function] is doable."

The low number of genes implies that comparative genomics will be a good way to understand gene function and which gene functions are conserved, added Christian Marcazzo, director of product marketing at Lion Bioscience.

But other comparative geneticists, namely those in academia, warn that the situation may not be so simple. The significance of the fewer-than-expected number of genes, some scientists said, lies in the complexity of gene networks and the post-translational modifications unique to human biology. Furthermore, the low number of uniquely human genes may be remarkable, but not proof that the genes we have in common with other animals act exactly the same way.

"It's not the number that matters at all; it's what the genes encode, how they are regulated, and what kinds of changes they have accumulated over eons of evolution," said Lisa Stubbs, who directs a mouse genomics research group at the Lawrence Livermore National Laboratory in Livermore, Calif.

And although humans may have 300 or so genes not found in mice, Stubbs said, the reverse is also true. "The mouse has plenty of genes that are not represented in humans," she said.

What accounts for the aspects of our physiology that make us distinctly human is not our 300 unique genes, but minor variations in gene networks, added William Loomis, a developmental biologist at the University of California, San Diego.

"Probably no new genes came into play as we developed our neural faculties. It probably occurred just as a modulation of existing networks," Loomis said.

Nevertheless, even the academics agreed on the importance of comparative techniques in determining the function of genes involved in common biochemical pathways.

"The amazing conservation of gene sequences and genome organizations among mammals, vertebrates, and other animals is remarkable. And it is these conserved features that allow information from all animals to provide strong suggestions about what human genes known only by sequence and position really do for us," said John Postlethwait, a zebrafish genomics researcher at the University of Oregon in Eugene.

Loomis put it more succinctly. "The fact that our genome is 95 percent similar [to the mouse] is wonderful," he said.

Marcazzo, of Lion, said his company is already acting to sieze on the opportunity the completed genome provides. Currently, Lion's GenomeScout software product performs similarity searches between microbial genomes, but Marcazzo said the company is developing the ability to make human-mouse and human-microbial comparisons. 

"To be able to say [a mouse gene] is an ortholog [of a human gene] gives more confidence going into the lab," he said. "Predictive tools can make people more comfortable making that decision."

Lexicon's Zambrowicz said the shift in research priorities from sequencing to functional genomics has not gone unnoticed by big pharma, and will undoubtedly stimulate interest in comparative studies. "They've spent a huge amount of money on identifying genes, and they're not going to let it go to waste," he said.

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