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New software streamlines the search for disease-causing genes

One of the greatest challenges in molecular medicine is identifying the genes that cause specific diseases often a painstaking process requiring months of laboratory trial and error. Now researchers have designed a computer program with the potential for dramatically speeding up the search for disease-causing genes and hastening the discovery of new drugs to treat a wide range of genetic illnesses.

The new software called Digital Disease is described in a study in the June 8 issue of the journal Science.

"The beauty of our software is that it runs in under a second on a computer instead of taking months to years in a lab," says Jonathan Usuka, a graduate student in chemistry and co-author of the Science study.

Usuka developed Digital Disease in collaboration with colleagues at the Roche pharmaceutical company, where he has been working as a part-time consultant while completing his doctoral dissertation.

Of mice and men

"The idea behind Digital Disease is shockingly simple," Usuka says. The software scans databases containing computerized maps of DNA molecules, then instantly locates irregularities in genes that might be responsible for cancer, diabetes and other ailments. Instead of searching through maps of the human genome, Digital Disease scans the DNA of mice, which are genetically similar to people.

"Human genes and mouse genes are about 80 percent identical," Usuka points out, "so if you can identify a genetic mutation in mice, you can easily locate the same mutation in humans."

Genes are located on chromosomes, which are actually molecules of DNA. Each gene, in turn, is made up of thousands of chemical subunits called nucleotides strung together in a specific sequence.

Every nucleotide contains one of four chemicals known by the abbreviations A, T, C and G. The order in which the four nucleotides occur determines how a gene functions and its ultimate effect on the physical makeup of both people and mice - everything f
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Contact: Mark Shwartz
mshwartz@stanford.edu
650-723-9296
Stanford University
6-Jun-2001


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