By Sean Henahan, Access Excellence

BALTIMORE- Researchers have developed a new "bar-coding" technique that allows the quantitative and simultaneous analysis of a large number of DNA transcripts. The new technique should speed the mapping of the human genome.

Called SAGE (for serial analysis of gene expression), this new method is analogous to the bar coding system used to catalog and monitor merchandise in grocery stores, says Kenneth W. Kinzler, Ph.D., Associate Professor of Oncology at Johns Hopkins, who led the research along with Bert Vogelstein, M.D., also at Johns Hopkins.

To better analyze the growing database of complementary DNA sequences (which represent DNA sequences that are complementary to RNA, and are thus functioning), the researchers developed a high-capacity system capable of monitoring the expression of many genes in parallel. The new method uses high-speed robotic printing of cDNAs onto glass which produces microarrays of high density cDNAs. The authors used this technique to monitor the gene expression patterns of 45 genes from the plant Aribodopsis thaliana.

"The series of black bars on the packaging of items in the grocery store is a code," says Kinzler. Each time this code is scanned at the cash register, a computer receives the information. At the end of the day, it can generate a report that tells how many times that particular product was purchased. In genetic terms, we would call this gene expression. If a product was frequently purchased, we would call it high expression, and if rarely purchased, we would call it low expression. The accumulated bar code entries provide a picture of the store's sales. By analogy, SAGE gives us a picture of the cell's gene expression pattern," says Kinzler.

Understanding the patterns of gene expression is the goal of much current biomedical research. Each human cell contains over 100,000 genes, but only a subset of the total genes is expressed in each cell. The specific subset of genes expressed determines the biologic properties of the cell--for example, whether the cell acts as part of the pancreas or part of the liver. In the new approach, the researchers assign a specific sequence of nine base pairs to each gene. These sequences are the "bar codes" that represent individual genes. These bar codes are then identified and counted by sophisticated sequencing and computer methods.

To demonstrate the technology, researchers at Hopkins and the Howard Hughes Medical Institute tested the method on pancreas and liver tissue. Once perfected, it took only a few days to obtain thousands of bar codes and identify genes that were specifically expressed in each of the two tissues. In addition to detecting expressed genes of known function, the scientists discovered several new genes.

The researchers plan to begin using the new technique to compare the gene expression patterns in colon cancer cells to those of normal colon cells to identify genes expressed only in the cancer cells. They hope these findings will lead to better methods of diagnosis and therapy. The technique should also prove useful in interpreting the large amounts of gene sequence data coming from the Human Genome Project. It should also provide new insights into the control of normal development.

The current research appeared in Science, Oct. 20, 1995, in articles by Schena et al; and Velculescu et al.

Related information on the Internet

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