Analyzing Thousands of Genes Simultaneously

Center for Expression Arrays Complements Older Techniques

The new UW Center for Expression Arrays (CEA), located in the Rosen Building in the south Lake Union neighborhood of Seattle, allows researchers to examine the expression of thousands of genes simultaneously. Microarray technology complements older techniques, which allow scientists to see changes in only a few genes at a time.

“This center can assist anybody on campus who is interested in gene expression. Almost anyone doing biology wants to know what genes are active in the cells that they are studying,” said Dr. Roger Bumgarner, the center’s director and a research assistant professor of microbiology.

The technology is important to a variety of biomedical studies ranging from specific disease research to developmental biology studies. The technology is also used to investigate the effects of exposure to drugs and toxins.

One satisfied customer is Dr. Theo Bammler, senior fellow in environmental health, who studies aflatoxin—a carcinogen present in poorly stored food products. Aflatoxin is associated with liver cancer and is considered a major public-health problem in some developing countries. Bammler and his colleagues want to know what genes are turned on and off in a healthy liver cell, as well as what genes are turned on and off in a cell exposed to aflatoxin. For the past several years, they have used traditional techniques to examine these changes one or two genes at a time.

In the Department of Microbiology, several researchers are using microarrays to study processes associated with viral or bacterial infection.

“One of the things we’re interested in is understanding what is going on in the host cell when it is infected,” Bumgarner said. “We’d like to do that with lots of different viruses and lots of different cells. We want to have a global view of the common strategies that viruses use to evade the host cell’s natural defenses.”

DNA slide

DNA samples on glass slides are indexed by a computer system at the UW Center for Expression Arrays. The gene expression data is then analyzed for information that contributes to a wide range of biomedical studies ranging from specific disease research to developmental biology studies.

The microarray center deposits 15,000 DNA samples on a microscope-sized glass slide with a precision robotics instrument—the Molecular Dynamics GenIII spotter. Each sample represents an individual gene and the center typically spots 7,500 genes in duplicate on each slide. (The amount varies. For human and mouse samples, the center spots about 7,500 genes, for yeast and pseudomonas, the center spots the entire genomes in duplicate on each slide).

The Array Spotter uses 12 capillary pens to deposit nanoliter volumes of samples onto coated slides, with an accuracy of 1 micron. The spotter is located within a case to keep the environment clean, and to maintain the humidity for the best spotting.

The overall effect on the slide is of a mosaic of dots, like a Pointillist painting. A computer indexing system keeps track of which dot is what DNA, and allows for complex data analysis. After all, each slide has up to 15,000 data points.

The copious amounts of microarray-generated data are analyzed by software. The center is planning to offer Affymetrix® arrays, a different form of the technology, in autumn 2001. The Affymetrix arrays are on silicon chips, which will expand the flexibility of the CEA’s offerings.

“Scientists here do end up with an enormous amount of data in a short time,” Bammler said. “Software and computer analysis is vital. There is no question that bioinformatics will continue to play an increasingly important role in the future.”

The CEA provides two days or more of training to researchers on campus to teach them how the array technology works, and how to prepare samples and analyze the subsequent data. Information about the CEA is available on-line.

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