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Category Archives: Genetic Medicine

Genetic sequencing gets faster, cheaper – and routine

Medicine appears poised to begin sequencing the entire genetic scripts of newborn babies with serious illnesses, a revolutionary change that was set in motion three years ago when scientists and doctors in Wisconsin used a similar technique to diagnose and treat a young Monona boy with a mysterious illness.

In a study released today in the journal Science Translational Medicine, researchers at Children's Mercy Hospitals and Clinics in Kansas City report that they used whole genome sequencing to diagnose babies born with serious genetic illnesses. Of the seven cases in which doctors used genome sequencing, six resulted in diagnoses.

Moreover, researchers said a diagnosis can be returned as quickly as 50 hours after a blood sample is taken from a baby, an important finding given that many of the diseases that afflict infants require very rapid treatment. That's much faster than the four to six weeks it had taken previously to go from sequencing to diagnosis.

Doctors at the Kansas City hospital said the test and accompanying analysis costs about $13,500 for each child and could present an appealing cost savings to health insurers. In the United States, thousands of babies each year with serious unknown diseases end up in the neonatal intensive care unit; there, beds cost some $8,000 a night and total expenses for one child can easily run to $250,000 or more.

"We think this is going to transform the world of neonatology," said Stephen Kingsmore, an author of the new paper and director of the Center for Pediatric Genomic Medicine at Children's Mercy Hospitals and Clinics. Kingsmore said his hospital will be using sequencing routinely for seriously ill newborns by the end of the year and will perform the same service for other hospitals around the country.

At Children's Hospital of Wisconsin and the Medical College of Wisconsin, where a similar newborn sequencing program quietly began two months ago, one of the doctors involved, read the new paper and declared "this is a huge leap forward.

"This is going to revolutionize our ability to take care of kids," added David Dimmock, a pediatric genetics specialist who worked on the team that sequenced young Nic Volker, of Monona, and crafted the treatment that appears to have saved the boy's life.

"The aim of this is to replace conventional testing with something that is faster and more comprehensive."

While the sequencing of Nic's genes in 2009 was used as a last resort after many other tests had been tried, the technology is now assuming a far more significant role in medicine. The hospital in Kansas City and Children's in Wisconsin are now using sequencing as a "first-line test," one that will save time and money over the current practice in which doctors hunt through a forest of individual tests for different diseases and mutations.

In Kansas City, doctors are focusing their sequencing program on a search for known mutations in known genes. Dimmock said the Wisconsin program has the added ability to detect new mutations such as the one that caused Nic's devastating intestinal disease. However, the Kansas City hospital gets results back faster - two days as opposed to a little more than a week in Wisconsin. Both hospitals have created special software programs that help doctors sift through the 3 million to 4 million variations in the genetic script of an average baby in order to find those most likely to have caused a disease.

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New, Faster Genetic Screen May Help Sick Babies

A new method of genetic testing appears to be able to help doctors diagnose critically ill babies more quickly than ever before, according to a new study.

The method allows doctors for decode a baby's entire genome in two days -- breathtakingly fast compared to current methods that can take six weeks or more.

In the new study, the researchers report using the approach to decode the entire genomes of six acutely ill newborns admitted to neonatal intensive care units, two of whom had already been determined to have genetic diseases. What they found in this proof of concept, they said, could be used in the future to more quickly diagnose sick newborns and treat them early.

The study was published Wednesday in the journal Science Translational Medicine.

"We think that we have come up with a solution for the tragic families who have a baby who's born and the doctors are not sure of what the cause of the baby's illness is," said the study's senior author, Dr. Stephen F. Kingsmore, director of the Center for Pediatric Genomic Medicine at Children's Mercy Hospitals and Clinics in Kansas City, Mo.

Many of the 3,500 known genetic diseases cause medical problems during the first month of life, the researchers wrote in their study. In the United States, over 20 percent of infant deaths are caused by genetic disorders and birth defects.

"Up to one third of babies admitted to a neonatal intensive care unit in the United States have genetic diseases," Kingsmore said, adding that babies with genetic problems often die or are sent home before a diagnosis is made.

For families coping with the tragedy of a sick newborn, the test may make a big difference.

"The family doesn't know what's going on," Kingsmore said. "The doctors are working heroically to figure out what's wrong. That can go on for weeks."

Armed with an early genetic diagnosis, Kingsmore said that doctors can communicate more clearly with the family.

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Genetic defect plays role in hearing loss too

Washington, Oct 1 (IANS) Going deaf? Blame a genetic mutation, linked with Usher syndrome type 1, says the latest finding, which could help develop more effective ways of treating this syndrome.

Usher syndrome is a genetic defect that causes deafness, night-blindness and a loss of peripheral vision through the progressive degeneration of the retina.

Researchers from the University of Cincinnati and Cincinnati Children's Hospital Medical Centre, partnered the study with the National Institute on Deafness and other Communication Disorders (NIDCD), Baylor College of Medicine and the University of Kentucky, the journal Nature Genetics reports.

"Researchers were able to pinpoint the gene which caused deafness in Usher syndrome type 1 as well as deafness that is not associated with the syndrome through the genetic analysis of 57 humans from Pakistan and Turkey," says Zubair Ahmed, assistant professor of ophthalmology from Cincinnati Children's and the study's lead investigator.

Ahmed says that a protein, called CIB2, which binds to calcium within a cell, is associated with deafness in Usher syndrome type 1 and non-syndromic hearing loss. "To date, mutations affecting CIB2 are the most common and prevalent genetic cause of non-syndromic hearing loss in Pakistan," he says, according to a Cincinnati statement.

"With this knowledge, we are one step closer to understanding the mechanism of mechano-electrical transduction and possibly finding a genetic target to prevent non-syndromic deafness as well as that associated with Usher syndrome type 1," Ahmed says.

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New Genetic Snooping Technique Finds New Deadly Virus

September 28, 2012

Image Caption: A Metabiota field staff member collects blood samples from bushmeat in the Democratic Republic of Congo. Credit: Metabiota

John Neumann for redOrbit.com Your Universe Online

An intriguing new virus from the Democratic Republic of Congo (DRC) has been identified as the cause of a deadly outbreak of acute hemorrhagic fever, which killed two people and left one gravely ill in the summer of 2009.

Described this week in the open-access journal PLoS Pathogens the new microbe has been named Bas-Congo virus (BASV) after the province in the southwest corner of the Congo where the three people lived.

The virus was first discovered when a teenager, living in the rural village of Mangala in the DRC, suddenly fell ill and developed symptoms of a hemorrhagic fever, including bleeding from mucous membranes and blood in the vomit. This victim died within three days of the first signs of illness.

A week later, a 13-year-old girl who attended the same school and lived in the same neighborhood came down with a similar illness and also died within three days, writes Nathan D. Wolfe, Joseph Fair, and Charles Chiu for National Geographic.

Known viruses, such as Ebola, HIV and influenza, represent just the tip of the microbial iceberg, explains Joseph Fair, PhD, a co-author and vice president of Metabiota. Identifying deadly unknown viruses, such as Bas-Congo virus, gives us a leg up in controlling future outbreaks.

These are the only three cases known to have occurred, although there could be additional outbreaks from this virus in the future, said Charles Chiu, MD, PhD, an assistant professor of laboratory medicine at UCSF and director of the UCSF-Abbott Viral Diagnostics and Discovery Center, who spearheaded the UCSF effort to identify the virus.

As a first step, Metabiota enlisted the help of close collaborator Dr. Eric Delwart at Blood Systems Research Institute (BSRI). Using sophisticated genetic sequencing techniques, Dr. Delwart detected a fragment of genetic information related to the rhabdovirus family.

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Four Distinct, Genetic Types of Breast Cancer, Study Finds

A new study on the genomics of breast cancer confirms that there are four distinct genetic types of the disease, suggesting that some drugs already used to treat cancer in other parts of the body could possibly be used to treat certain forms of breast cancer that share the same genetic abnormalities.

The researchers, whose findings were published Sunday in the journal Nature, studied the DNA of breast cancer tumors of 825 patients at various stages of the disease, and found that the disease could be stratified into four major genetic categories.

The study, a collaborative effort between 348 researchers, is part of a larger project known as the Cancer Genome Atlas, which is mapping the genetic changes in 20 cancers, including breast cancer. The new study, part of the largest breast cancer genomic project, offers the largest pool of data for researchers who have known for decades that there were genetic subtypes of breast cancer.

"This again reconfirms on a larger scale the heterogeneity that exists between each patient's breast cancer," said Dr. Ben Park, associate professor of oncology at the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins. Park was not involved in the study.

The genetic analysis not only included a comprehensive look at the inherited basis for the cancers but also examined how proteins expressed within the genes affected the type of cancers that were classified.

"We now understand the recoding of the genome that is behind [these cancers]," said Dr. Matthew Ellis, a professor of medicine at Washington University in St. Louis, and a researcher on the study. The Cancer Genome Atlas work "lays the foundation for a new and much more informed approach to developing cures for all our patients," he said.

In particular, researchers found that one type of the disease, more commonly known as triple negative breast cancer, genetically resembles a form of ovarian cancer that is currently treatable. Triple negative breast cancer is an aggressive and deadly form of the disease that responds to chemotherapy but has high rates of relapse.

But clinicians caution that it will take years for these initial genetic findings to change the course of treatment for breast cancer, which is expected to kill nearly 40,000 women in 2012, according to the American Cancer Society.

"You would need to treat a large number of patients with this profile to see whether the hypothesis works," said Dr. Jay Brooks, chairman of the department of hematology and oncology at Ochsner Clinic Foundation and Hospital in Baton Rouge, La. Brooks was not affiliated with the study.

According to many breast cancer experts, the findings confirm that cancers should be defined and treated according to their genetic components rather than their location in the body.

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New Studies On Genetic Variations Offer Insights Into Origins Of Man

April Flowers for redOrbit.com Your Universe Online

Thousands of years ago, a genetic mutation occurred which might be the answer to how early humans were able to move from central Africa and across the continent. This movement has been called the great expansion.

Three teams of researchers, from Wake Forest Baptist Medical Center, Johns Hopkins University School of Medicine and University of Washington School of Medicine, have analyzed genetic sequence variation patterns in different populations around the world. Their research, published this week in the online journal PLoS One, demonstrates that about 85,000 years ago, a critical genetic variant arose in a key gene cluster on chromosome 11, known as the fatty acid desaturase cluster (FADS).

This genetic variant would have allowed humans to convert plant-based polyunsaturated fatty acids (PUFAs) to brain PUFAs. The long-chain of PUFAs found in the brain are necessary for increased brain size, complexity and function, and the FADS cluster plays a critical role in determining how effectively medium-chain PUFAs in plants are converted.

According to archeological and genetic studies, Homo sapiens appeared approximately 180,000 years ago. For almost 100,000 years, our early ancestors tended to stay in one location close to bodies of water in central Africa. Scientists have hypothesized that this location was critical because early humans needed large amounts of the long-chain PUFA docosahexaenoic acid (DHA) commonly found in fish and shellfish in order to support complex brain function.

This may have kept early humans tethered to the water in central Africa where there was a constant food source of DHA, explained Dr. Floyd Chilton, director of the Center for Botanical Lipids and Inflammatory Disease Prevention at Wake Forest Baptist.

There has been considerable debate on how early humans were able to obtain sufficient DHA necessary to maintain brain size and complexity. Its amazing to think we may have uncovered the region of genetic variation that arose about the time that early humans moved out of this central region in what has been called the great expansion.

Under the intense pressure of natural section, this new trait was able to spread rapidly throughout the entire Homo sapiens population on the African continent.

The power of genetics continually impresses me, and I find it remarkable that we can make inferences about things that happened tens of thousands of years ago by studying patterns of genetic variation that exist in contemporary populations, said Dr. Joshua M. Akey from the University of Washington.

The most important result of this conversion was that humans no longer had to rely on just one food source, fish, for brain growth and development. This was particularly important because the genetic variant arose before organized hunting and fishing could have provided more reliable sources of long-chain PUFAs.

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