Daily Archives: March 12, 2014

CHICAGO -- These days, it's faster and cheaper than ever to decipher a person's entire DNA. But a small study suggests that looking for disease risks that way may not be ready for the masses.

For one thing, the research found that gene variants most likely linked with significant disease were the least likely to be accurately identified.

And analyzing the mass of data from the DNA scan is a daunting task, researchers said.

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Stanford University researchers performed whole genome sequencing in 12 healthy people. Most of the millions of genetic variants they found were of uncertain significance, although one woman was found to have a high genetic risk for cancer.

DNA is recovered by a simple blood test and deciphered by machines. The difficulty lies in interpreting the findings and figuring out which variants are important and which ones can be ignored. That takes days of sophisticated follow-up lab tests and interpretation to reveal potentially meaningful genetic information, the researchers said.

Dr. Euan Ashley, a senior co-author and Stanford associate professor of medicine and genetics, likened the technology to "an unruly teenager who has grown up very fast. There's huge potential."

"This paper is like parental tough love -- we have to be really honest about where we are in order to bring it up to clinical standards," he said.

For the test, they used two commercially available instruments to sequence the DNA - the second one to validate the initial findings. But less than one-third of variants in inherited disease genes were confirmed.

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Could genome sequencing become routine at doctor's offices?

Before doctors use technology to evaluate every "letter" in a person's DNA to detect or diagnose medical conditions, several hurdles must be overcome, according to a new study.

Researchers found that sequencing a person's whole genome - all three billion or so DNA nucleotides in the chromosomes - required a significant amount of manpower for a small payoff.

They also found that identifications of potentially significant variations were not always reliable and doctors disagreed on how to proceed.

One of the study's authors said the cost of sequencing a person's entire genome has dropped in recent years, but the technology has been mostly used for research.

"We thought the time had come to do a small pilot study of patients in the clinical setting," Dr. Euan Ashley told Reuters Health.

Ashley is a specialist in genomics and medicine at the Stanford School of Medicine in California.

For the new study published in JAMA, he and his colleagues recruited 12 unrelated people between November 2011 and March 2012 to have their full genomes sequenced.

The goal was to see how whole-genome sequencing may work in a real-world setting, such as a hospital or doctor's office.

After drawing blood from the participants, the researchers sent all twelve samples to be sequenced by one large company and nine of the samples were also sent to a second sequencing company to see how comparable the sequence results would be.

The two sets of sequences mostly agreed when it came to common genetic variants (versions) of genes, but there were greater differences in the results among less common variants. For about 10 percent to 19 percent of genes that may be related to inherited diseases, the sequences were not reliable enough to ensure accuracy.

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Challenges remain before docs use whole-genome sequencing to diagnose disease

Once the most popular gamebird in the nation, the bobwhite quail has suffered huge population losses, an alarming trend that has been noted for decades.

Now, researchers at Texas A&M University are hopeful that a high-intensity project to decode the plump little bird's entire genome will help its long-term chances for survival.

Chris Seabury, a genetics professor at A&M's Department of Veterinary Medicine and Biomedical Sciences, led a research team that recently finished the first "draft genome assembly" for a wild bobwhite quail.

"By sequencing and assembling the bobwhite quail genome, the team produced the most comprehensive resource currently available for cutting-edge interdisciplinary research in the bobwhite," Seabury said in a prepared statement.

The peer-reviewed research was published Wednesday in the March 2014 issue of the open-access scientific journal PLOS ONE.

Nicknamed Pattie Marie, the quail whose leg muscle tissue provided DNA for the research, was donated by a Texas hunter, Seabury said.

Other A&M members of the team were Professor Ian Tizard, director of the Schubot Exotic Bird Health Center; Donald Brightsmith, professor with the Schubot center; A&M research assistants Yvette Halley and Eric Bhattarai.

The project, which took two years to complete, also involved research colleagues Jerry Taylor and Jared Decker, University of Missouri; Charles Johnson and Dale Rollins, A&M AgriLife Research; and Markus Peterson, A&M's Department of Wildlife and Fisheries Sciences.

Two private-industry scientists, Scot E. Dowd and Paul M. Seabury, also took part.

Once the DNA was isolated, it was then fragmented for sequencing, Seabury said by email.

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A&M research could stop bobwhite quail's alarming decline