Featured Research

from universities, journals, and other organizations

Taking the gamble out of DNA sequencing: How much can be learned in a large-scale experiment

Date:
February 24, 2013
Source:
University of Southern California
Summary:
Scientists have developed an algorithm to predict how much can be learned in a large-scale DNA sequencing experiment -- with potential applications in every field of science.

Two USC scientists have developed an algorithm that could help make DNA sequencing affordable enough for clinics -- and could be useful to researchers of all stripes.

Andrew Smith, a computational biologist at the USC Dornsife College of Letters, Arts and Sciences, developed the algorithm along with USC graduate student Timothy Daley to help predict the value of sequencing more DNA, to be published in Nature Methods on February 24.

Extracting information from the DNA means deciding how much to sequence: sequencing too little and you may not get the answers you are looking for, but sequence too much and you will waste both time and money. That expensive gamble is a big part of what keeps DNA sequencing out of the hands of clinicians. But not for long, according to Smith.

"It seems likely that some clinical applications of DNA sequencing will become routine in the next five to 10 years," Smith said. "For example, diagnostic sequencing to understand the properties of a tumor will be much more effective if the right mathematical methods are in place."

The beauty of Smith and Daley's algorithm, which predicts the size and composition of an unseen population based on a small sample, lies in its broad applicability.

"This is one of those great instances where a specific challenge in our research led us to uncover a powerful algorithm that has surprisingly broad applications," Smith said.

Think of it: how often do scientists need to predict what they haven't seen based on what they have? Public health officials could use the algorithm to estimate the population of HIV positive individuals; astronomers could use it to determine how many exoplanets exist in our galaxy based on the ones they have already discovered; and biologists could use it to estimate the diversity of antibodies in an individual.

The mathematical underpinnings of the algorithm rely on a model of sampling from ecology known as capture-recapture. In this model, individuals are captured and tagged so that a recapture of the same individual will be known -- and the number of times each individual was captured can be used to make inferences about the population as a whole.

In this way scientists can estimate, for example, the number of gorillas remaining in the wild. In DNA sequencing, the individuals are the various different genomic molecules in a sample. However, the mathematical models used for counting gorillas don't work on the scale of DNA sequencing.

"The basic model has been known for decades, but the way it has been used makes it highly unstable in most applications. We took a different approach that depends on lots of computing power and seems to work best in large-scale applications like modern DNA sequencing," Daley said.

Scientists faced a similar problem in the early days of the human genome sequencing project. A mathematical solution was provided by Michael Waterman of USC, in 1988, which found widespread use. Recent advances in sequencing technology, however, require thinking differently about the mathematical properties of DNA sequencing data.

"Huge data sets required a novel approach. I'm very please it was developed here at USC," said Waterman.

This research was funded by grants from the National Institutes of Health National Human Genome Research Institute (R01 HG005238 and P50 HG002790).


Story Source:

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


Journal Reference:

  1. Timothy Daley, Andrew D Smith. Predicting the molecular complexity of sequencing libraries. Nature Methods, 2013; DOI: 10.1038/nmeth.2375

Cite This Page:

University of Southern California. "Taking the gamble out of DNA sequencing: How much can be learned in a large-scale experiment." ScienceDaily. ScienceDaily, 24 February 2013. <www.sciencedaily.com/releases/2013/02/130224142825.htm>.
University of Southern California. (2013, February 24). Taking the gamble out of DNA sequencing: How much can be learned in a large-scale experiment. ScienceDaily. Retrieved July 30, 2014 from www.sciencedaily.com/releases/2013/02/130224142825.htm
University of Southern California. "Taking the gamble out of DNA sequencing: How much can be learned in a large-scale experiment." ScienceDaily. www.sciencedaily.com/releases/2013/02/130224142825.htm (accessed July 30, 2014).

Share This




More Plants & Animals News

Wednesday, July 30, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

Raw: Otters Enjoy Water Slides at Japan Zoo

Raw: Otters Enjoy Water Slides at Japan Zoo

AP (July 30, 2014) River otters were hitting the water slides to beat the summer heatwave on Wednesday at Ichikawa City's Zoological and Botanical Garden. (July 30) Video provided by AP
Powered by NewsLook.com
In Virginia, the Rise of a New Space Coast

In Virginia, the Rise of a New Space Coast

AP (July 30, 2014) Every summer, tourists make the pilgrimage to Chincoteague Island, Va. to see wild ponies cross the Assateague Channel. But, it's the rockets sending to supplies to the International Space Station that are making this a year-round destination. (July 30) Video provided by AP
Powered by NewsLook.com
Rodents Rampant in Gardens Around Louvre

Rodents Rampant in Gardens Around Louvre

AP (July 29, 2014) Food scraps and other items left on the grounds by picnickers brings unwelcome visitors to the grounds of the world famous and popular Louvre Museum in Paris. (July 29) Video provided by AP
Powered by NewsLook.com
Jane Goodall Warns Great Apes Face Extinction

Jane Goodall Warns Great Apes Face Extinction

AFP (July 29, 2014) The world's great apes face extinction within decades, renowned chimpanzee expert Jane Goodall warned Tuesday in a call to arms to ensure man's closest relatives are not wiped out. Duration: 00:58 Video provided by AFP
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:
from the past week

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