UCSD Jacobs School of Engineering
University of California San Diego

Genetic Basis of Human Disease

While one Jacobs School professor is exploring how to reduce the cost of sequencing genomes (story at left), another has developed a tool to facilitate mapping the genetic basis of complex diseases such as Alzheimer's and multiple sclerosis.

"Genome-wide analysis may soon become a standard methodology in the search for more effective, individualized treatments," predicts computer science and engineering professor Eleazar Eskin.

An expert in bioinformatics, Eskin co-developed the HAP Webserver to give scientists more insight into genetic variation. The Internet service simplifies a computational task to predict the variation on each chromosome (as opposed to what is collected by scientists using highthroughput technology, which mixes the information from both chromosomes). Scientists from around the world have uploaded nearly 6,000 genotypes to the HAP Webserver, which computed their inferred haplotypes—the sequences of nucleotide bases in each copy of the chromosome.

For one study published in Science , Eskin used the HAP Webserver to process more than 190 million data points derived from the DNA of 71 individuals of European American, African American and Han Chinese American ancestry.

"Using other programs, haplotyping would require at least a few months of CPU time," says Eskin. "But we were able to use a cluster of computers from Calit2's OptIPuter project to perform our final entire analysis in less than 12 hours."

Eskin now routinely does haplotyping of large international genotype databases. He is also working on potential commercial extensions of the software, with support from the von Liebig Center.

Related Links
News Release: California computer scientists double volume of data in NIH biotech repository. 10/26/05
Website: HAP Webserver
Website: Zarlab: Eleazar Eskin Group
Website: Undergraduate Research in Bioinformatics
In This Issue
Towards a $1,000 genome sequencing test
Studying genomes of the sea
Palsson's system: calculating the sum of a cell's parts
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