Microarray Test to Identify Hundreds of Biologic Threats

A new biodefense microarray test that can detect hundreds of top-priority bacterial and viral biologic threats such as anthrax and plague is being developed, funded by a U.S.$2.1 million grant from the U.S. National Institute of Allergy and Infectious Diseases (NIAID). The array appears to foreshadow the future of routine patient testing as well.

The new arrays, expected to work in as little as four hours, offer three advantages over old testing methods. First, the array will offer a comprehensive single-step test to simultaneously identify genetic fingerprints for 26 different bacterial species, 10 viral species, and hundreds of their subspecies, so the array can take the place of dozens of existing tests.

A second advantage is that the array will detect DNA from a deadly pathogen that has been inserted into an apparently harmless bacteria, which could be missed by traditional identification methods. For example, if a section of plague DNA was inserted into common escherichia coli bacteria, traditional tests might only detect the E coli, missing the newly engineered pathogen and allowing the threat to go unchecked. The microarray will test for 56 different toxic genes from bacteria.

The third advantage over old testing methods is that the array will detect whether or not genes that make organisms resistant to antibiotics have been inserted into a pathogen. If an antibiotic resistance gene goes undetected, doctors could end up treating patients with medication that simply wouldn't work. Using current methods, researchers have to test for every antibiotic resistance gene one at a time. The microarray tests for 62 genes simultaneously.

This single comprehensive test is possible because of recent advances in the GeneChip microarray technology of Affymetrix (Santa Clara, CA, USA; www.affymetrix.com) that enables researchers to analyze millions of different DNA strands on a chip the size of a thumbnail. Although there is a pressing need for this technology in biodefense, the ultimate application will be in the doctor's office, where arrays could be used to identify hundreds of more common, naturally occurring pathogens, such as streptococcus or hepatitis, enabling doctors to quickly diagnose a patient's illness.

Researchers expect to have a prototype array in three months, with a multi-pathogen array expected to be commercially available within three years. The Affymetrix resequencing technology used in this array is identical to that used in the company's severe acute respiratory syndrome (SARS) and smallpox arrays developed earlier in 2004.

"Instead of diagnosing a disease by using a hundred different tests, microarray technologies will allow us to perform all of those tests at the same time using a single tool,” said Carsten Rosenow, Ph.D., senior scientist, Genomic Collaborations at Affymetrix. "Quick, precise diagnosis by DNA analysis is going to help provide more precise treatments at lower costs, and reduce human suffering around the world.”


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