Category Archives: Genome

Peshawar Startup Genome

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TUESDAY, March 11, 2014 (HealthDay News) -- Commercially available tests can analyze your genetic profile and try to predict your risk of a host of diseases. But a new study suggests they aren't ready for prime time.

The technology, known as whole-genome sequencing, allows scientists to "map" the information encoded in most of the billions of building blocks that make up a person's DNA.

So far, whole-genome sequencing has been used mainly in research. But the hope is that the technology will help fuel a new era of "personalized medicine" -- where doctors will be able to identify patients with gene variants that raise their risk of certain diseases.

In the past few years, the cost of whole-genome sequencing has fallen to the point where it could soon be feasible to use it in everyday health care, said Dr. Frederick Dewey, of Stanford University, the lead researcher on the new study.

But based on his team's findings, Dewey said, a lot more work is needed before that idea becomes reality.

The study, reported in the March 12 issue of the Journal of the American Medical Association, found that sequencing a whole genome remains a fairly daunting task.

And although the commercially available tests are good, they aren't yet reliable enough for routine patient care, Dewey said.

For the study, Dewey's team recruited 12 healthy adults who volunteered a blood sample for whole-genome sequencing.

Overall, testing showed that each patient had between 2 million and 3 million unique variations in their DNA. The researchers then used a software program they had developed to whittle down that sea of information to around 100 genetic variations per person that were deemed worthy of more investigation.

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Whole-Genome Scans Not Quite Ready for Widespread Use: Study

March Teaser - Cosmic Genome
A look inside the March edition of Cosmic Genome featuring Prof Alice Roberts, Lewis Dartnell, Brian Cox, Robin Ince and more. To get the full edition of The...

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Source: Public Affairs Alliance of Iranian Americans (PAAIA)

Washington, D.C. - Dr. Pardis Sabeti MD/Ph.D., professor at Harvard University and MITs Broad Institute, has had the opportunity to study the genetics of many different populations throughout her storied career. But one population missing from the genetics research done by Dr. Sabeti and others is her own - the Iranian population. Genetics research has advanced medicine in many ways - from identifying new drug targets to allowing scientists to identify the cause of some cancers. Understanding the genetics of the Iranian population would be the first step to ensuring Iranians are a part of the personalized medicine that has resulted from genetics research. We are in the midst of a revolution in the fields of genomics and medicine, and it is thrilling to bring this to bear for my own heritage, said Dr. Sabeti.

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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

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?

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

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Both the technical barriers associated with human DNA sequencing and the costs involved have been decreasing for some time. A new study investigates the benefits and drawbacks of whole genome sequencing in clinical applications.

The first sequencing of a human genome began in 1990 and was completed in 2003 at a cost of $2.7 billion. Now, whole genome sequencing (WGS) can cost as little as $1,000, with the procedure taking just days.

When sequencing an organism's DNA, the order of DNA nucleotides is documented by machines. This ordering is transcribed in letters - A, C, G and T - which each represent a particular piece of DNA (adenines, guanines, thyamines and cytosines). The human genome is made up of 3 billion of these letters.

Using the genome sequence, scientists are able to find genes much more easily. In a clinical setting, it is hoped that WGS could quickly and accurately reveal the genetic basis of family diseases. Even in healthy individuals, it is believed that WGS can uncover potentially important information about a person's genes and their health.

For example, Medical News Today recently reported on new research that looked at using WGS to select embryos for in vitro fertilization.

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Whole genome sequencing 'not ready for widespread clinical use'

13 hours ago Mar. 11, 2014 - 2:41 PM PDT

Everyday access to the contents of our genes draws nearer and nearer. But the industry is currently complicated by a mix of rapidly advancing technology and just-emerging science: Despite the fact that we can read our genes, we dont necessarily know what they mean.

A Stanford University study that will be published tomorrow in theJournal of the American Medical Associationtook a look at whole-genome sequencing for clinical use and found that it has more substantial obstacles to overcome than many people might realize.

We need to be very honest about what we can and cannot do at this point in time, paper co-author Euan Ashley said in a release. Our hope is that the identification of specific hurdles will allow researchers in this field to focus their efforts on overcoming them to make this technique clinically useful.

The Stanford team evaluated obstacles by sequencing the genomes of 12 healthy people. They then manually analyzed about 100 genetic variations in each person. It took an hour for each variation to determine if it might increase the risk for disease.

After looking at each of the variations, the researchers settled on two to six per person that merited a follow up test. One test participant found out she was at risk for breast and ovarian cancer.

Although there are clearly challenges in bringing whole-genome sequencing into the clinic, this finding was clearly medically significant, co-lead paper author Frederick Dewey said in the release. Its not possible to predict from a study of 12 people how often this type of clinically actionable discovery will occur, but it definitely supports the use of this technology.

But catching that one instance of disease risk came at a great cost: 100 hours of labor, which boosted the cost of sequencing to $17,000. Three genetic counselors, three clinicians and one medical pathologist pored over each of the results because there is no straightforward way to determine if a single gene mutation poses a risk. Instead, the team consulted medical literature and made the call if all of a patients gene mutations together called for a follow up test. Follow ups costfrom $351 to $776.

The team also found that it is impossible for currently available off-the-shelf tests to achieve the same level of accuracy in genome sequencing.

These off-the-shelf genome sequencing techniques were developed to provide generally good coverage of most of the genome, Dewey said in the release. But there are some regions that remain to be covered well that we care very deeply about. We still need to supplement this information with additional sequencing in some regions to make clinically usable decisions.

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Cheap, reliable whole-genome sequencing? Not so fast, say Stanford researchers

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Current technology for sequencing a person's whole genome does not always capture data on key genes.

Sequencing a persons entire genome can reveal potentially life-saving information about the presence of mutations associated with diseases. But there are drawbacks a study published this week finds that current sequencing technology does not always capture the complete genome, and illustrates the challenges of interpreting what the results mean for an individual patient1.

There are many steps that have to be worked out to ensure that we gain the most health-care benefit, says William Feero, a physician at the Maine Dartmouth Family Medicine Residency in Fairfield, Maine, who was not involved in the study.

Researchers at Stanford University in California, examined whether a whole-genome scan could identify disease risks in healthy people a use of the technology that is within financial reach as the cost of sequencing drops.

The team of doctors, genetic counsellors and scientists report today in the Journal of the American Medical Association that it sequenced the whole genomes of 12 people with no diagnosed genetic diseases, looking for genetic mutations that might cause disease. Every patient was found to have 26 such mutations, and one woman found out that she carried a mutation in the gene BRCA1, which is linked to greater risk of ovarian and breast cancer. She opted to have her ovaries removed as a result.

But the researchers, led by cardiologists Euan Ashley and Thomas Quertermous, also found that between the two genome sequencing services they used Illumina, based in San Diego, California, and Complete Genomics, based in Mountain View, California 1019% of genes known to be linked to disease were not adequately sequenced. So doctors might have missed finding harmful mutations in these genes. The two services also disagreed two-thirds of the time about the presence of a particularly worrisome type of mutation the addition or deletion of parts of genes linked to disease.

Deciding what these results meant for patients was not easy. The study clinicians often disagreed about what patients should do in light of the findings about their genomes for instance, whether a particular mutation meant that the patient should undergo further testing.

Were very excited about the idea that genome sequencing can transform medicine, Ashley says. We need to apply some tough love and be really honest about what we can be confident about with this technology and what still needs a bit of work.

On the bright side, the researchers found that the cost of whole-genome sequencing was lower than they expected. Ashley estimates it costs about US$11,000 to sequence one persons genome and interpret the data. Follow-up testing for people in the study cost less than $1,000 per person, indicating that the adoption of whole-genome sequencing is not unleashing a flood of expensive downstream procedures.

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Genome sequencing stumbles towards the clinic