Speed-Reading the Genome

Reading genomes is a messy business. Even the terminology—like "shotgun"—evokes images of inelegant science. But Woburn, Mass.-based US Genomics plans to change that. Inventor Eugene Chan based the GeneEngine™ on the same mechanisms cells use to read DNA. He designed a system in which DNA is first linearized and then threaded through a nanofluidic chip at high speeds. Before the analysis, the DNA sample is treated with a set of fluorescently labeled tetramers that cover the thr

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The result is a device with the potential to analyze a single, long strand of DNA. That means far less handling of DNA and therefore fewer problems with contamination and loss. Chan claims that it is also faster than existing systems; it analyzes 10 to 30 million base pairs per second. And best of all, he says, the system may not require polymerase chain reaction (PCR).

The US Patent and Trademark Office recently awarded US Genomics patent No. 6,355,420, "Methods and products for analyzing polymers," to cover its GeneEngine technology. Though the system isn't commercially available yet, the company has entered into collaborations with the Wellcome Trust Sanger Institute and Pui-Yan Kwok, dermatology professor at the University of California, San Francisco, to validate its claims and enhance further development.

The GeneEngine is a potentially powerful tool for haplotype analysis, says Kwok. In haplotype analysis, scientists correlate inheritance of a disease ...

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