Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:


RAD-tagging technology is demystifying genome sequencing

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,

Jim Barlow | EurekAlert!
Further information:

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

More articles from Life Sciences:

nachricht Novel mechanisms of action discovered for the skin cancer medication Imiquimod
21.10.2016 | Technische Universität München

nachricht Second research flight into zero gravity
21.10.2016 | Universität Zürich

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

Im Focus: New 3-D wiring technique brings scalable quantum computers closer to reality

Researchers from the Institute for Quantum Computing (IQC) at the University of Waterloo led the development of a new extensible wiring technique capable of controlling superconducting quantum bits, representing a significant step towards to the realization of a scalable quantum computer.

"The quantum socket is a wiring method that uses three-dimensional wires based on spring-loaded pins to address individual qubits," said Jeremy Béjanin, a PhD...

Im Focus: Scientists develop a semiconductor nanocomposite material that moves in response to light

In a paper in Scientific Reports, a research team at Worcester Polytechnic Institute describes a novel light-activated phenomenon that could become the basis for applications as diverse as microscopic robotic grippers and more efficient solar cells.

A research team at Worcester Polytechnic Institute (WPI) has developed a revolutionary, light-activated semiconductor nanocomposite material that can be used...

Im Focus: Diamonds aren't forever: Sandia, Harvard team create first quantum computer bridge

By forcefully embedding two silicon atoms in a diamond matrix, Sandia researchers have demonstrated for the first time on a single chip all the components needed to create a quantum bridge to link quantum computers together.

"People have already built small quantum computers," says Sandia researcher Ryan Camacho. "Maybe the first useful one won't be a single giant quantum computer...

Im Focus: New Products - Highlights of COMPAMED 2016

COMPAMED has become the leading international marketplace for suppliers of medical manufacturing. The trade fair, which takes place every November and is co-located to MEDICA in Dusseldorf, has been steadily growing over the past years and shows that medical technology remains a rapidly growing market.

In 2016, the joint pavilion by the IVAM Microtechnology Network, the Product Market “High-tech for Medical Devices”, will be located in Hall 8a again and will...

Im Focus: Ultra-thin ferroelectric material for next-generation electronics

'Ferroelectric' materials can switch between different states of electrical polarization in response to an external electric field. This flexibility means they show promise for many applications, for example in electronic devices and computer memory. Current ferroelectric materials are highly valued for their thermal and chemical stability and rapid electro-mechanical responses, but creating a material that is scalable down to the tiny sizes needed for technologies like silicon-based semiconductors (Si-based CMOS) has proven challenging.

Now, Hiroshi Funakubo and co-workers at the Tokyo Institute of Technology, in collaboration with researchers across Japan, have conducted experiments to...

All Focus news of the innovation-report >>>



Event News

#IC2S2: When Social Science meets Computer Science - GESIS will host the IC2S2 conference 2017

14.10.2016 | Event News

Agricultural Trade Developments and Potentials in Central Asia and the South Caucasus

14.10.2016 | Event News

World Health Summit – Day Three: A Call to Action

12.10.2016 | Event News

Latest News

Novel mechanisms of action discovered for the skin cancer medication Imiquimod

21.10.2016 | Life Sciences

Second research flight into zero gravity

21.10.2016 | Life Sciences

How Does Friendly Fire Happen in the Pancreas?

21.10.2016 | Life Sciences

More VideoLinks >>>