Featured Research

from universities, journals, and other organizations

New Process Makes Genome Sequencing More Efficient

Date:
May 9, 2002
Source:
University Of Georgia
Summary:
Sometimes the genius of a discovery lies in how its parts are put together. University of Georgia scientists have combined existing technologies in a unique way that could revolutionize genetic research, saving countless time and hundreds of millions of dollars. The discovery? Bring back a once-important but now rarely used molecular technique and combine it with newer cloning and DNA sequencing methods. The effect is a dramatic leap in efficiency.

Sometimes the genius of a discovery lies in how its parts are put together. University of Georgia scientists have combined existing technologies in a unique way that could revolutionize genetic research, saving countless time and hundreds of millions of dollars.

Related Articles


The discovery? Bring back a once-important but now rarely used molecular technique and combine it with newer cloning and DNA sequencing methods. The effect is a dramatic leap in efficiency.

"It can reduce the cost of sequencing entire genomes by 50 to 95 percent," said Andrew Paterson, director of the UGA Plant Genome Mapping Laboratory (www.plantgenome.uga.edu) and a professor of crop and soil sciences, botany and genetics.

That kind of savings could be staggering. Sequencing the sorghum genome, used as an example to develop the new Cot-based Cloning and Sequencing (CBCS) method, would cost about $7.5 million, compared to $20 million with the current "shotgun" approach.

The difference is in the number of clones required to be sequenced. Sequencing the onion genome would require 119 million clones. CBCS slashes that to 15 million, eliminating the immense time and $354 million in funding required to do the other 104 million. For the sugar pine, CBCS cuts 281 million required clones to 60 million, knocking down costs by $750 million.

The thing that drives up the time and cost to sequence a genome is its vast number of relatively meaningless DNA sequences. "Repetitive sequences complicate all aspects of gene and genome research," Paterson said.

These highly repetitive sequences are, in essence, genetic junk, said Daniel Peterson, research coordinator with the Plant Genome Mapping Lab. There may be thousands, even millions, of copies of a single sequence. One such sequence, for example, is repeated nearly a million times in the human genome, accounting for nearly 10 percent of human DNA.

"Most of these are ancient viruses," Peterson said. "They're 'selfish DNA' making up much of the bulk of a genome but adding nothing to its genetic complexity."

The problem is that to sequence an entire genome, scientists have to wade through these endless copies to get to the genes, which virtually always come in only one or a few copies each.

A technique called Cot analysis makes the savings possible. Developed in the 1960s and widely used in the '70s, it was all but abandoned with the advent of molecular cloning methods. In the late '80s and '90s, research based on Cot analysis bottomed out.

One reason it fell into disuse is that even in the rarefied world of molecular biology, it's a highly demanding process. "You have to be very careful in interpreting the data," Peterson said.

Peterson has been an ardent defender of the value of Cot analysis. The method splits the double strands of DNA into single strands, or denatures them, and then allows them under controlled conditions to renature, or recouple into double strands.

Cot analysis breaks down a complex genome into three populations: highly repetitive (HR), moderately repetitive (MR) and single- or low-copy (SL) sequences. It's based on the principle that the more highly repetitive sequences will renature faster.

The UGA scientists' breakthrough came when Paterson suggested cloning the separate populations. That made it much easier to separate out, and sequence, the low-copy DNA that includes most of the genes and regulatory ("on-off") switches. "It's like shooting fish in a barrel," Peterson said.

The approach allows researchers to focus their time and funds on the single- and low-copy sequences, which comprise a small part of the genome but virtually all of its information content.

Paterson, Peterson and eight other UGA scientists have published their CBCS findings in a May article in Genome Research. Susan Wessler, who specializes in the HR sequences, is named with Paterson and Peterson in UGA's application for a patent on the CBCS method.


Story Source:

The above story is based on materials provided by University Of Georgia. Note: Materials may be edited for content and length.


Cite This Page:

University Of Georgia. "New Process Makes Genome Sequencing More Efficient." ScienceDaily. ScienceDaily, 9 May 2002. <www.sciencedaily.com/releases/2002/05/020507073423.htm>.
University Of Georgia. (2002, May 9). New Process Makes Genome Sequencing More Efficient. ScienceDaily. Retrieved November 23, 2014 from www.sciencedaily.com/releases/2002/05/020507073423.htm
University Of Georgia. "New Process Makes Genome Sequencing More Efficient." ScienceDaily. www.sciencedaily.com/releases/2002/05/020507073423.htm (accessed November 23, 2014).

Share This


More From ScienceDaily



More Health & Medicine News

Sunday, November 23, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

WFP: Ebola Risks Heightened Among Women Throughout Africa

WFP: Ebola Risks Heightened Among Women Throughout Africa

AFP (Nov. 21, 2014) Having children has always been a frightening prospect in Sierra Leone, the world's most dangerous place to give birth, but Ebola has presented an alarming new threat for expectant mothers. Duration: 00:37 Video provided by AFP
Powered by NewsLook.com
Could Your Genes Be The Reason You're Single?

Could Your Genes Be The Reason You're Single?

Newsy (Nov. 21, 2014) Researchers in Beijing discovered a gene called 5-HTA1, and carriers are reportedly 20 percent more likely to be single. Video provided by Newsy
Powered by NewsLook.com
Raw: Paralyzed Marine Walks With Robotic Braces

Raw: Paralyzed Marine Walks With Robotic Braces

AP (Nov. 21, 2014) Marine Corps officials say a special operations officer left paralyzed by a sniper's bullet in Afghanistan walked using robotic leg braces in a ceremony to award him a Bronze Star. (Nov. 21) Video provided by AP
Powered by NewsLook.com
Milestone Birthdays Can Bring Existential Crisis, Study Says

Milestone Birthdays Can Bring Existential Crisis, Study Says

Newsy (Nov. 21, 2014) Researchers find that as people approach new decades in their lives they make bigger life decisions. Video provided by Newsy
Powered by NewsLook.com

Search ScienceDaily

Number of stories in archives: 140,361

Find with keyword(s):
Enter a keyword or phrase to search ScienceDaily for related topics and research stories.

Save/Print:
Share:

Breaking News:

Strange & Offbeat Stories


Health & Medicine

Mind & Brain

Living & Well

In Other News

... from NewsDaily.com

Science News

Health News

Environment News

Technology News



Save/Print:
Share:

Free Subscriptions


Get the latest science news with ScienceDaily's free email newsletters, updated daily and weekly. Or view hourly updated newsfeeds in your RSS reader:

Get Social & Mobile


Keep up to date with the latest news from ScienceDaily via social networks and mobile apps:

Have Feedback?


Tell us what you think of ScienceDaily -- we welcome both positive and negative comments. Have any problems using the site? Questions?
Mobile: iPhone Android Web
Follow: Facebook Twitter Google+
Subscribe: RSS Feeds Email Newsletters
Latest Headlines Health & Medicine Mind & Brain Space & Time Matter & Energy Computers & Math Plants & Animals Earth & Climate Fossils & Ruins