Student publishes case for faster, less expensive DNA analysis

Jun 27, 2011

A Washington State University student's undergraduate research is challenging a widely held assumption on the best way to analyze old DNA in anthropological and forensic investigations.

Sarah "Misa" Runnells' claim is weighty enough to be published this week in the peer-reviewed, online journal .

At issue is the best way to sequence "ancient" DNA, bits of pulled from remains up to 800,000 years old. Such remains tend to be chemically degraded, making it difficult to draw accurate connections between, say a wooly mammoth and modern animals, or and humans.

The techniques are also an issue in forensic investigations where remains, while relatively new, can still be severely compromised.

In 2000, researchers writing in the journal Science recommended a set of standards that emphasized cloning bits of to detect errors and contamination from modern DNA.

"Those rules became gospel," says Brian Kemp, a WSU and . In fact, they became so widely adopted that his preferred technique—direct sequencing—is often dismissed by journal reviewers.

"I've had papers outright rejected because they said, 'You did not clone,'" says Kemp.

Kemp wanted to demonstrate that direct sequencing worked just as well by directly comparing it to cloning, but he had a problem: He didn't have experience with cloning.

Then he met Runnells, who had learned to clone while majoring in biotechnology as a WSU undergraduate. The two used both methods to analyze 3,500-year-old northern fur seal bones.

"After five samples with both cloning and direct sequencing, we got the same answer from both methods," says Runnells, who has published under her soon-to-be married name of Winters.

Their findings even held up with one particularly degraded sample. Cloning gave conflicting DNA sequences in the sample, while direct sequencing showed gaps in the code.

"In no case did the results of one method conflict with another," says Kemp.

The PLoS ONE paper is the first published on a $595,000 grant Kemp received from the U.S. Department of Justice. One goal of the grant is to find more cost-effective ways of analyzing degraded DNA.

Direct sequencing can cost a fraction of cloning and be done in less time, says Kemp.

"That's really applicable to the justice system, where you want to save money and time," says Runnells, who is now a second-year Master's student in zoology.

"Everybody wants to save money and time," adds Kemp. "There are more forensic cases than they can work on. There's a backlog of forensic cases."

Direct sequencing can also be increasingly helpful to academic researchers in a time of shrinking budgets, says Kemp.

"If you have an infinite amount of resources and funding, you can do anything," he says. "You can clone everything a thousand times. It doesn't matter. But for the assistant professor at WSU who has a limited budget, we need to make smart choices."

Explore further: Chickens to chili peppers: Scientists search for the first genetic engineers

More information: "To clone or not to clone: Method analysis for retrieving consensus sequences in ancient DNA samples":

Provided by Washington State University

4.6 /5 (5 votes)

Related Stories

DNA: Yes, Snuppy is definitely a clone

Mar 08, 2006

Seoul National University scientists investigating the work of disgraced cloning pioneer Woo Suk Hwang have found Snuppy is a genuine cloned dog.

Genetic Material under a Magnifying Glass

Jan 28, 2008

The genetic alphabet contains four letters. Although our cells can readily decipher our genetic molecules, it isn’t so easy for us to read a DNA sequence in the laboratory. Scientists require complex, highly sophisticated ...

Closing the gaps in the human genome

Jun 01, 2009

Sequence gaps in human chromosome 15 have been closed by the application of 454 technology. Researchers writing in BioMed Central's open access journal Genome Biology have described a simple and scalable method for finish ...

Recommended for you

Deadly human pathogen Cryptococcus fully sequenced

9 hours ago

Within each strand of DNA lies the blueprint for building an organism, along with the keys to its evolution and survival. These genetic instructions can give valuable insight into why pathogens like Cryptococcus ne ...

Building better soybeans for a hot, dry, hungry world

Apr 16, 2014

( —A new study shows that soybean plants can be redesigned to increase crop yields while requiring less water and helping to offset greenhouse gas warming. The study is the first to demonstrate ...

User comments : 1

Adjust slider to filter visible comments by rank

Display comments: newest first

not rated yet Jun 28, 2011
can this direct sequencing detect DNA that has been faked (seeing as I recently saw an article explaining how it is possible to now fake DNA evidence)?

More news stories

Deadly human pathogen Cryptococcus fully sequenced

Within each strand of DNA lies the blueprint for building an organism, along with the keys to its evolution and survival. These genetic instructions can give valuable insight into why pathogens like Cryptococcus ne ...

Biologists help solve fungi mysteries

( —A new genetic analysis revealing the previously unknown biodiversity and distribution of thousands of fungi in North America might also reveal a previously underappreciated contributor to climate ...

Better thermal-imaging lens from waste sulfur

Sulfur left over from refining fossil fuels can be transformed into cheap, lightweight, plastic lenses for infrared devices, including night-vision goggles, a University of Arizona-led international team ...

Hackathon team's GoogolPlex gives Siri extra powers

( —Four freshmen at the University of Pennsylvania have taken Apple's personal assistant Siri to behave as a graduate-level executive assistant which, when asked, is capable of adjusting the temperature ...