Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

RAD-tagging technology is demystifying genome sequencing

27.04.2011
University of Oregon researchers document how their technique quickly puts a genome together

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 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, Johnson and UO colleague 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 it along the way as sequencing tools advanced, Johnson, Cresko and three UO colleagues provide a proof-of-principle paper in the April issue of PLoS One, a publication of the Public Library of Science. The National Institutes of Health-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," 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, Johnson said: "We first asked if we can piece together one short sentence at a time instead of ordering all the words in the whole book at once. Next, can we put together one paragraph at a time? That's like going from, say, 1,000 letters of the genome in a row to 5,000 at a time. Here, we show that we can do this. We can put the book back together."

A RAD marker in the book analogy might be a word at the start of each sentence. Using that marker as an anchor, the rest of the words in the sentence are easily separated from all the words in the book, and then the words in the sentence are put in the right order, on an on until all the content is organized correctly, Johnson said. The end product, he added, contains few, if any, leftover or unexplained fragments, a problem occurring with current technologies that rely on clusters of computers, requiring extensive memory, to complete sequencing projects.

RAD technology can be applied to study the genetics of organisms for which genomes have not been completed, Johnson said.

The PLoS One paper detailed how RAD works on stickleback and the bacterium e-coli. Both involve small and rather simple genomes. There already is interest in its potential application in human genome sequencing, Johnson said.

At about the same time the PLoS One paper was being published, Johnson, who also is the chief scientific officer of Floragenex, was part of a company-sponsored, one-day RAD Sequencing and Genomics Symposium in Portland, Ore., on April 19. Nine researchers from five institutions (UO, Oregon State University, University of British Columbia, University of Tennessee and University of Washington) described how they are applying RAD in their sequencing projects.

"It was quite gratifying to hear them speak about this technology and how it is working for them," Johnson said.

RAD technology also is being used in a three-year project -- funded by a $1 million grant from the W.M. Keck Foundation and led by Cresko and UO colleague Hui Zong -- to identify genetic changes that occur from the formation of a single mutation to full-fledged cancer. The project could lead to a new generation of molecular diagnostics to detect cancers in their earliest stages.

Co-authors of the PLoS One paper with Johnson and Cresko were Paul D. Etter, a postdoctoral researcher, and doctoral student Jessica L. Preston, both of Johnson's lab, and Susan Bassham, a postdoctoral researcher in Cresko's lab.

About the University of Oregon

The University of Oregon is among the 108 institutions chosen from 4,633 U.S. universities for top-tier designation of "Very High Research Activity" in the 2010 Carnegie Classification of Institutions of Higher Education. The UO also is one of two Pacific Northwest members of the Association of American Universities.

Source: Eric A. Johnson, associate professor of biology, 541-346-5183, eajohnsn@uoregon.edu

Jim Barlow | EurekAlert!
Further information:
http://www.uoregon.edu

Further reports about: DNA marker Floragenex PLoS One RAD technology RAD-tagging

More articles from Life Sciences:

nachricht Antimicrobial substances identified in Komodo dragon blood
23.02.2017 | American Chemical Society

nachricht New Mechanisms of Gene Inactivation may prevent Aging and Cancer
23.02.2017 | Leibniz-Institut für Alternsforschung - Fritz-Lipmann-Institut e.V. (FLI)

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Breakthrough with a chain of gold atoms

In the field of nanoscience, an international team of physicists with participants from Konstanz has achieved a breakthrough in understanding heat transport

In the field of nanoscience, an international team of physicists with participants from Konstanz has achieved a breakthrough in understanding heat transport

Im Focus: DNA repair: a new letter in the cell alphabet

Results reveal how discoveries may be hidden in scientific “blind spots”

Cells need to repair damaged DNA in our genes to prevent the development of cancer and other diseases. Our cells therefore activate and send “repair-proteins”...

Im Focus: Dresdner scientists print tomorrow’s world

The Fraunhofer IWS Dresden and Technische Universität Dresden inaugurated their jointly operated Center for Additive Manufacturing Dresden (AMCD) with a festive ceremony on February 7, 2017. Scientists from various disciplines perform research on materials, additive manufacturing processes and innovative technologies, which build up components in a layer by layer process. This technology opens up new horizons for component design and combinations of functions. For example during fabrication, electrical conductors and sensors are already able to be additively manufactured into components. They provide information about stress conditions of a product during operation.

The 3D-printing technology, or additive manufacturing as it is often called, has long made the step out of scientific research laboratories into industrial...

Im Focus: Mimicking nature's cellular architectures via 3-D printing

Research offers new level of control over the structure of 3-D printed materials

Nature does amazing things with limited design materials. Grass, for example, can support its own weight, resist strong wind loads, and recover after being...

Im Focus: Three Magnetic States for Each Hole

Nanometer-scale magnetic perforated grids could create new possibilities for computing. Together with international colleagues, scientists from the Helmholtz Zentrum Dresden-Rossendorf (HZDR) have shown how a cobalt grid can be reliably programmed at room temperature. In addition they discovered that for every hole ("antidot") three magnetic states can be configured. The results have been published in the journal "Scientific Reports".

Physicist Dr. Rantej Bali from the HZDR, together with scientists from Singapore and Australia, designed a special grid structure in a thin layer of cobalt in...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

Booth and panel discussion – The Lindau Nobel Laureate Meetings at the AAAS 2017 Annual Meeting

13.02.2017 | Event News

Complex Loading versus Hidden Reserves

10.02.2017 | Event News

International Conference on Crystal Growth in Freiburg

09.02.2017 | Event News

 
Latest News

From rocks in Colorado, evidence of a 'chaotic solar system'

23.02.2017 | Physics and Astronomy

'Quartz' crystals at the Earth's core power its magnetic field

23.02.2017 | Earth Sciences

Antimicrobial substances identified in Komodo dragon blood

23.02.2017 | Life Sciences

VideoLinks
B2B-VideoLinks
More VideoLinks >>>