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Category Archives: Genetic Medicine

Powerful new method to analyze genetic data

ScienceDaily (June 12, 2012) University of Texas Medical Branch at Galveston researchers have developed a powerful visual analytical approach to explore genetic data, enabling scientists to identify novel patterns of information that could be crucial to human health.

The method, which combines three different "bipartite visual representations" of genetic information, is described in an article to appear in the Journal of the American Medical Informatics Association. The work won a distinguished paper award when it was presented at the AMIA Summit on Translational Bioinformatics in March 2012.

In the paper, the authors use their technique to analyze data on genetic alterations in humans known as single-nucleotide polymorphisms, or SNPs. Among other things, the frequencies of particular SNPs are associated with an individual's ancestral origins; for the study, the researchers chose to examine SNP data from 60 individuals from Nigeria and 60 individuals from Utah.

"We selected SNPs that we already knew differentiated between the two groups, and then showed that our method can reveal more about the data than traditional methods," said UTMB associate professor Suresh Bhavnani, lead author on the JAMIA paper and a member of UTMB's Institute for Translational Sciences. "This is a fresh way of looking at genetic data, a methodological contribution that we believe can help biologists and clinicians make better sense of a variety of biomarkers."

Like many kinds of biomedical data, Bhavnani said, datasets describing individuals and their SNPs are particularly suited to visual representations that are bipartite: that is, they simultaneously present two different classes of data. In the case of the Utah-Nigeria SNP data, Bhavnani and his colleagues started with what is known as a bipartite network visualization -- an intricate computer-generated arrangement of colored dots and black, gray and white lines.

"In the bipartite network you see both the individuals and their genetic profiles simultaneously, and cognitively that's really important," Bhavnani said. "You can look at the individuals and know immediately which SNPs make them different from others, and conversely you can look at the SNPs to see how they are co-occurring, and with which individuals they are co-occurring. This rich representation enables you to quickly comprehend the complex bipartite relationships in the data"

The bipartite network visualization of the Utah-Nigeria individual-SNP data has distinct clusters on its left and right sides that correspond to the Utah and Nigerian subjects and SNPs. It also accurately portrays a genetic phenomenon called admixture, in which an individual possesses SNPs that are characteristic of individuals from Utah as well as from Nigeria. Admixed individuals are placed on the edges of their clusters, relatively close to the center of the visualization. The identification of admixed individuals, and the implicated SNPs could help in the design of case-control studies where there is a need for the selection of homogenous sets of individual from different ancestral origins.

To produce an even more detailed picture of the individual-SNP information, the researchers applied two other bipartite visualization techniques to the data: the bipartite heat map, and the bipartite Circos ideogram. In the heat map, rectangular cells laid out in a spreadsheet-like arrangement and colored white, gray, or black helped precisely define the boundaries of the clusters by clarifying individual-SNP relationships. In the Circos ideogram, individuals and SNPs placed around the perimeter of a circle and linked with curved lines, enabling the researchers to more closely examine the admixed individuals' ties to SNPs in the clusters associated with both Utah and Nigeria.

"The network representation is very powerful because it gives you the overall structure of the data, but to really understand the complex relationships, you need these additional bipartite representations," Bhavnani said.

The JAMIA paper, according to Bhavnani, represents a proof of concept for the researchers' novel combination of methods, which can be applied to a wide range of biomedical questions. "You can think of anything -- for example you could examine cases and controls in Alzheimer's disease, or you could compare children who are prone to ear infections and those aren't prone," Bhavnani said. "Whatever your disease or trait of interest is, our approach can handle it."

Powerful new method to analyze genetic data

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Scientists Find New Genetic Path to Deadly Diarrheal Disease

Newswise ATHENS, Ohio (June 11, 2012)Scientists have found new genetic information that shows how harmful bacteria cause the acute diarrheal disease shigellosis, which kills more than a million people worldwide each year.

The research, which could lead to the development of future treatments, was published today in the journal PLoS ONE. The study was led by Ohio University scientist Erin Murphy and doctoral student William Broach, with contributions from University of Nevada, Las Vegas and University of Texas at Austin researchers.

When the disease-causing bacterium Shigella invades a human host, environmental conditions there, such as changes in temperature or pH, stimulate a genetic expression pathway within the bacterium that allows it to survive and cause disease. Central to this genetic pathway are two proteins, VirF and VirB. VirF functions to increase production of VirB which, in turn, promotes the production of factors that increases the bacteriums virulence, or ability to cause illness in its host.

Its like a domino effect, said Murphy, assistant professor of bacteriology in the Ohio University Heritage College of Osteopathic Medicine.

Murphy and Broachs new study, however, suggests that production of VirB can be controlled independently of VirF. It also shows that the VirF-independent regulation is mediated by a specific small RNA, a special type of molecule whose job is to control the production of particular targets. This is the first study to demonstrate that transcription of virB is regulated by any factor other than VirF, Murphy explained.

The research not only reveals the intricate level of gene expression the bacteria employ to survive in the human body, but potentially could lead to new treatments. Currently, antibiotics are prescribed to patients with the disease.

These findings are feeding into the basic understanding of this gene expression so that future researchers can work to disrupt it, Broach said. The more we know about it, the more targets we have to disrupt it and to possibly develop targeted antibiotic treatments.

For those living in developing countries, where access to clean drinking water can be scarce, an improved medical treatment for shigellosis could mean the difference between life and death.

In the United States, if we get severe diarrhea we can go to the store and get Gatorade, Murphy said. But if you're already starving to begin with because you don't have access to good food and clean water, then you get shigellosis on top of thatand you dont have good water to rehydrate yourselfthats when the deaths happen.

The disease, which is transmitted person to person or through contaminated food or water sources, has an infectious dose of just 10 organisms, meaning as few as 10 organisms can cause disease in a healthy person. This infectious dose is exceedingly low compared to other bacteria that require tens of thousands of organisms to cause disease.

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Prenatal genetic test offers more information, raises questions – Mon, 11 Jun 2012 PST

June 11, 2012 in Health, Health,Features

Deborah L. Shelton Chicago Tribune (MCT)

The latest advance in prenatal genetic testing purports to offer parents more detailed information than ever about the child they are expecting. But for some, the new answers could lead to another round of questions.

The technology allows doctors to detect small or subtle chromosomal changes in a fetus such as missing or extra pieces of DNA that could be missed by standard tests.

Most parents will get results confirming a normal pregnancy. But some will learn that their baby has a birth defect, a developmental problem or other medical condition, and in a small number of cases the test will detect things that no one knows quite how to interpret.

The information can allow parents to prepare for early intervention and treatment, but it also could raise questions about terminating the pregnancy or lead to nagging worry over uncertain results.

The Reproductive Genetics Institute in Chicago, which has helped pioneer the rapidly developing field of prenatal diagnosis and testing, recently began offering the procedure array comparative genomic hybridization, or array CGH for short to any pregnant woman who wants it.

The technology has been available for a number of years but it has almost never been used prenatally, said Dr. Norman Ginsberg, an obstetrician specializing in prenatal genetic testing at the institute. We think this is the beginning of the next generation of how well look at things.

Other medical experts see the technology as promising but have concerns about using it as a first-line test because of the potential drawbacks and the lack of published research. The availability of array CGH also raises fundamental, sometimes delicate, questions for parents.

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Prenatal genetic test offers more information, raises questions - Mon, 11 Jun 2012 PST

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Welcome to Gattaca: Genetic Discrimination Becomes Reality – Video

09-06-2012 16:05 06/07-08/2012 Mom gave a blood sample. Dad spit. The entire genome of their fetus was born. Researchers at the University of Washington have, for the first time, done a near-total genome sequence of a fetus in this way. Scientists published the results of this study in the journal Science Translational Medicine, suggesting that thousands of genetic diseases could be detected in children while they are still in the fetal stage. More:

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Genetic testing doesn’t drive up demand for more health services

Patients who have genetic testing done to detect their risk for multiple health conditions do not use more health services after testing than those who elect not to be checked, says a study published online May 17 in Genetics in Medicine.

Genetic tests increasingly are being marketed directly to patients, raising concerns among some physicians that they could cause a spike in patients requesting unnecessary screening and procedures, said Robert J. Reid, MD, PhD, lead study author and associate investigator with Group Health Research Institute in Seattle.

Certainly, there is a lot of concern in the country that doing indiscriminate testing of individuals around their genetic susceptibility will alarm them and increase demand, he said.

Researchers studied 1,599 insured patients between age 25 and 40 from the Henry Ford Health System in Detroit. Of those, 217 opted to get genetic tests. Patients who received the tests had more specialty physician visits before the checks than the untested group, but the study found no change in overall use of health care services among those who had the evaluations done and those who did not (

Researchers analyzed health care usage by participants for 12 months before and 12 months after genetic testing. Dr. Reid said the study took a conservative approach. It looked only at screening and procedures associated with four of eight conditions whose risk could be detected from the multiplex genetic susceptibility tests: type 2 diabetes mellitus, atherosclerotic coronary heart disease, colorectal cancer and lung cancer. Also, the tests were thoroughly explained to all study participants something that doesnt necessarily happen in everyday practice, Dr. Reid said.

They certainly had a fair amount of material on which to base their decision, and they had follow-up to help them understand the results, he said. In most cases there is not a lot of counseling beforehand or a lot of explanation afterward.

One surprising factor was how few patients opted to have the testing done, Dr. Reid said.

Blacks were significantly less likely than whites to choose testing, as were those with just a high school education or less. The age group studied could be a factor, as younger individuals may feel that such tests offer little value at that stage in their lives, he said.

More research needs to be done to determine how genetic tests impact behavior in larger groups of patients. Such tests may have a positive impact by motivating some patients to make healthier lifestyle choices.

If someone is told they are at risk for heart disease or diabetes, it might prompt them to maintain a healthy body weight, try to lower their cholesterol or stop smoking, Dr. Reid said. I think that is the next stage to see if it promotes positive health behavior.

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Genetic testing doesn’t drive up demand for more health services

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Scientists map baby’s genetic code in womb

Scientists map babys genetic code in womb

By John von Radowitz

Friday, June 08, 2012

An unborn babys whole genetic code has been mapped in the womb using DNA taken from its parents.

The technique could in future make it possible to swiftly scan for some 3,500 genetic disorders before birth, without physically disturbing either foetus or mother.

But scientists acknowledge the ability to sequence a babys whole genome in the womb has as yet unresolved ethical implications.

It could produce a wealth of data relating to a babys future health. At the same time, difficult questions may be raised about the moral case for termination.

Most pre-natal genetic screening currently involves tapping fluid from the foetal sac, or taking placental samples. Such invasive methods can only identify a small number of birth defects including Downs syndrome, and spina bifida.

They also pose risks for both mother and child. But there are thousands of rarer genetic conditions that are seldom spotted until they start producing symptoms.

The new research involved analysing DNA shed by the foetus and floating in the mothers bloodstream. Blood sample DNA from the mother was also studied as well as DNA extracted from the fathers saliva.

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Scientists map baby’s genetic code in womb

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