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UCSB Neuroscientists Receive New Device To Aid Genetics Research



UCSB’s Neuroscience Research Institute recently acquired an innovative gene sequencer that is capable of sequencing the human genome — a task that used to take years — in a matter of hours.

A gene sequencer allows researchers to work toward advancing medical development and biological research by determining the exact order of nucleotides within a molecule of DNA. The new acquisition makes UCSB the first campus in the UC system to own such a device.

Assistant Research Scientist Monte Radeke of the NRI said this more accessible method of gene sequencing could be used to discover genetic connections to diseases.

“In essence, it has a capability of sequencing a whole human genome in one crack,” Radeke said. “Typically the instrument would be used to find differences in the human genome between individuals, and eventually you want to associate those differences with disease.”

Radeke said the sequencer is unique in that it uses semiconducter technology to work. A semiconductor chip with two large wells is filled with a given sample, then spun in a centrifuge, effectively scattering the single sample across many microscopic wells on the chip’s surface with excess draining away.

The chip, laden with the sample, is then inserted into the gene sequencing machine. Small pipes flood in one type of nucleotide at a time, calling for Adenine, Guanine, Cytosine and Thymine, on demand. When ‘A’ is flooded in, every ‘A’ in the sample will give off a proton as it incorporates the new incoming ‘A.’ The protons are then measured and recorded by the machine in a manner analogous to the way a digital camera measures light and thus records it in pixels.

This allows the sequencing computer, with several terabytes worth of computing space, to determine the sequence of nucleotides in the sample. For one chip, this process takes about four seconds, according to Radeke.

Researchers repeat the process again and again, and within hours, the entire human genome is sequenced.

The Human Genome Project, which marked the first time the human genome was ever sequenced, took years to complete and cost millions of dollars. Now, the process can be completed in a few hours at a much cheaper price. Each semiconductor chip costs between $500 and $1000, with the reusable sequencer itself priced at under $1 million.

Radeke said once the device has sequenced a genome, the results can be compared to others to determine the differences and variations between them, which could shed light on how certain diseases are genetically coded.

“If you find a gene whose expression level goes way up or way down in the presence of a certain disease, there’s a reasonable chance that the expression level in that gene might be associated with the disease,” Radeke said. “By comparing a normal tissue to a diseased tissue, we’re trying to tease out the mechanisms that cause those diseases.”

Once genetic markers for certain diseases are determined, a healthy individual’s genome can be sequenced to find out the chances of developing the disease.

UCSB researcher and co-director of the NRI Kenneth Kosik will be using the sequencer to study the genetic causes of Alzheimer’s disease, while Radeke’s lab is looking at age-related macular degeneration.

 

A version of this article appeared on page 1 of February 4th, 2013’s print edition of the Nexus.

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