By Aliyah Kovner
Campus News Reporter
In the pursuit of cementing its reputation as a top research institution, UC Santa Cruz obtained a cutting-edge gene sequencing machine in July.
The university was able to collect the funds thanks to grants from STEPS Institute for Innovation in Environmental Research, the National Institutes of Health and other organizations. Funding also came straight from the pockets of professors, including project leader Nader Pourmand of biomolecular engineering.
The machine is of the newest generation of sequencing technology, called an ABI SOLiD analyzer. It replaces the less efficient Sanger series.
It is the cutting-edge machine for bioinformatics — the technology has only been available for two years.
“This machine produces high-output DNA sequences with much-reduced cost in comparison to the traditional Sanger, and is more accurate than other next-generation sequencing technologies currently available,” said Alex Tajlil, bioinformatics computer analyst. Tajlil is a graduate of the University of Glasgow, Scotland, who is conducting research at UCSC.
The machine costs over $500,000, with supplementary expenses for the equipment used alongside the sequencer. In addition to computer software that interprets the results, the SOLiD analyzer requires two technicians, who had to be trained for two weeks. Even with grants, UCSC researchers did not have enough to make the purchase.
“I saw that many other campuses have one of those big, next-generation sequencers machines,” Pourmand said, “so I collected over 20 signatures across the departments, and put together the grant proposal.”
The equipment adds to the prestige of the Genome Sequencing Center (GSC), which is directed by Pourmand.
GSC works in collaboration with the Genome Browser, a breakthrough technology that launched Professor David Haussler into the biology spotlight.
Pourmand’s group is part of QB3, University of California’s Institute for Quantitative Biomedical Research, which also assisted in funding. The collaboration is between three UC campuses: Santa Cruz, San Francisco and Berkeley.
Pourmand’s group’s focus is on disease correlation, which compares the DNA of people with genetic diseases with that of people who do not have those diseases. They also work with metagenomics, which evaluates microbial DNA from environmental samples.
“We can check the difference between one type of tuberculosis and a drug-resistant one, see where the variations are,” Pourmand said. “If we know where the variations are we can find out how to treat them, how to make better drugs.”
The equipment will benefit numerous other research groups, such as Tajlil’s, which provides the secondary analysis of the machine output.
“There is going to be a close collaboration between Pourmand’s laboratory and different parts of UCSC,” Tajlil said.
When the collaboration begins, Tajlil hopes to improve the browser to accommodate more differences in genes. The sequencer looks at samples of human DNA to understand diseases. The bigger the range in alleles — one member of a gene pair — the more comprehensive the results will be.
“UCSC is already a major biotech hub, and our new techniques will definitely underline that,” Tajlil said.
At present, Haussler’s lab is working on stem cell maturation, changes in the genome of cancer cells, and recent evolutionary genetic changes in the human genome.
Haussler said, “The range of applications for this unique technology at UCSC is significant.”