New technology can test thousands of DNA samples


On a glass slide is a chip with the DNA of 38,000 viruses and 3,500 bacteria. Wash it with a test sample and in less than 24 hours time, it will tell you whether that sample contains any of those bugs. It's called a Microbial Detection Array. It has potential in biodefense. It has potential in the doctor's office.

"It can tell you quickly in a clinical setting what infection people have, whether it's viral or bacterial," says Crystal Jaing.

Jaing is one of a team of Lawrence Livermore biologists, computer scientists and statisticians who are developing the technology.

"It can be used for product safety," she adds, "such as a study we did of a rotavirus vaccine. It can tell you how clean a commercially available product is and improve the safety of products."

In fact, it played an important role in confirming the discovery of a pig virus (benign) that was hiding inside a vaccine for children. "We were very surprised to find this virus in the vaccine," Jaing says. "This was very unexpected."

Product safety regulations don't require a drug manufacturer to know everything that is in a medication, just certain harmful things that are not. However, this technology could, for the first time, enable them to know everything that's in a drug and its concentration. That's new.

The study validated a powerful new technology developed by a team at Lawrence Livermore National Laboratory including Jaing, fellow biologist Shea Gardner and computer scientist Kevin McLoughlin.

Imagine a microscopic checkerboard with more than a million squares on it. Each square holds a probe for a different sequence of genes. Dipped in a soup of sample DNA, those probes will stick to their matching genes in the sample. In a big blue box (the GenePix4000!), a laser scans the checkerboard and displays every square with a match.

No test on the market can do what this lab can, with its multidisciplinary approach and supercomputers. But, a desktop version is possible.

"Definitely," according to Jaing. "That is something that we are very interested in. Right now we have the microarray. We would like to develop that into an instrument so it can go into the hospital, where it can do clinical diagnostics."

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