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New software streamlines the search for disease-causing genes

ata from the earlier studies, the software predicted the chromosome locations with remarkable accuracy.

For example, in lab mice with lymphoma, Digital Disease correctly predicted the three chromosomal regions known to carry lymphoma-causing genes. The software also pinpointed a fourth gene location, which may open up a new avenue of lymphoma research, according to Usuka.

Digital Disease also predicted the four chromosomal regions known to contain asthma-causing genes, along with two other potential asthma gene sites.

"We showed that we can predict computationally in a second what other studies took months or years to do," notes Usuka. "We believe that, with our software, you can reduce the search to about 10 percent of the mouse genome, which will save a huge amount of time."

Finding the precise location of disease-causing genes will require additional lab work, he points out, but the new software should give medical researchers a tremendous head start.

"Genetic experiments churn through hundreds of inbred lab mice, but our system minimizes that need. With only a handful of mice, you have an answer in a second, then youre off and running," Usuka says.

Frat boy mice

Besides diseases, the software also was successful in locating chromosomal regions containing genes that determine various physical traits, such as bone mineral density, eye weight and even alcohol preference what Usuka calls "frat boy mice" versus "teetotaler mice."

"With our software and the SNP database we are making public, if you know any physical or behavioral trait, youll be able to find what part of the mouse genome that trait might come from," Usuka explains. The new software even works in reverse.

"We can actually predict how mice look, how theyll behave, whether they like alcohol or whether theyre susceptible to lymphoma and other diseases," he says. "A lot of geneticists dont believe this can be done, especially with only 3,000 SNPs, then theyre amazed when they
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Contact: Mark Shwartz
mshwartz@stanford.edu
650-723-9296
Stanford University
6-Jun-2001


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