RAD Technology May Simplify Genome Sequencing

Take millions of puzzle pieces containing partial words and put them back together into full words, sentences, paragraphs and chapters until the book these random parts came from is rebuilt. That daunting process in not unlike sequencing an organism's genome, says University of Oregon biologist Dr. Eric A. Johnson, a member of the UO Institute of Molecular Biology. His lab developed a patent-pending technology for discovering differences between genomes called restriction-site associated DNA markers, or RAD. They have now shown that RAD can also be used to help put a genome sequence together. The original RAD technique, unveiled in 2005, led to the UO spinoff company Floragenex, which uses the technology in plant genetics. More recently, Dr. Johnson and UO colleague Dr. William A. Cresko used it to identify genetic differences in threespine stickleback, a fish, which evolved separately after environmental conditions had isolated some of the saltwater fish into freshwater habitats. Now, after three years of research, adapting the technology along the way as sequencing tools advanced, Dr. Johnson, Dr. Cresko, and three UO colleagues provide a proof-of-principle paper published online on April 13, 2011, in PLoS One. The NIH-funded research documents that the new method, called RAD paired-end contigs, works and provides accurate sequencing results. "The RAD sequence is a placeholder that identifies one small region of a genome," Dr. Johnson said. "We showed that this technique lets us gather together appropriate nearby sequences and piece them together." In just seconds, a section is completed, he said. In a matter of hours, he added, an entire genome's sequence emerges. Using the book analogy, Dr.
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