Monthly Archives: February 2014

Whole Genome Analysis, STAT

Posted: February 19, 2014 at 7:46 pm

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Newswise Although the time and cost of sequencing an entire human genome has plummeted, analyzing the resulting three billion base pairs of genetic information from a single genome can take many months.

In the journal Bioinformatics, however, a University of Chicago-based teamworking with Beagle, one of the worlds fastest supercomputers devoted to life sciencesreports that genome analysis can be radically accelerated. This computer, based at Argonne National Laboratory, is able to analyze 240 full genomes in about two days.

This is a resource that can change patient management and, over time, add depth to our understanding of the genetic causes of risk and disease, said study author Elizabeth McNally, MD, PhD, the A. J. Carlson Professor of Medicine and Human Genetics and director of the Cardiovascular Genetics Clinic at the University of Chicago Medicine.

The supercomputer can process many genomes simultaneously rather than one at a time, said first author Megan Puckelwartz, a graduate student in McNallys laboratory. It converts whole genome sequencing, which has primarily been used as a research tool, into something that is immediately valuable for patient care.

Because the genome is so vast, those involved in clinical genetics have turned to exome sequencing, which focuses on the two percent or less of the genome that codes for proteins. This approach is often useful. An estimated 85 percent of disease-causing mutations are located in coding regions. But the rest, about 15 percent of clinically significant mutations, come from non-coding regions, once referred to as junk DNA but now known to serve important functions. If not for the tremendous data-processing challenges of analysis, whole genome sequencing would be the method of choice.

To test the system, McNallys team used raw sequencing data from 61 human genomes and analyzed that data on Beagle. They used publicly available software packages and one quarter of the computers total capacity. They found that shifting to the supercomputer environment improved accuracy and dramatically accelerated speed.

Improving analysis through both speed and accuracy reduces the price per genome, McNally said. With this approach, the price for analyzing an entire genome is less than the cost of the looking at just a fraction of genome. New technology promises to bring the costs of sequencing down to around $1,000 per genome. Our goal is get the cost of analysis down into that range.

This work vividly demonstrates the benefits of dedicating a powerful supercomputer resource to biomedical research, said co-author Ian Foster, director of the Computation Institute and Arthur Holly Compton Distinguished Service Professor of Computer Science. The methods developed here will be instrumental in relieving the data analysis bottleneck that researchers face as genetic sequencing grows cheaper and faster.

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Whole Genome Analysis, STAT

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Eczema Diet – A Curing Eczema Juice – Video

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Eczema Diet - A Curing Eczema Juice
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Suffering From Eczema and Dry Itchy Skin? Get Rid of Them by Eliminating Internal Toxins! – Video

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Suffering From Eczema and Dry Itchy Skin? Get Rid of Them by Eliminating Internal Toxins!
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Suffering From Eczema and Dry Itchy Skin? Get Rid of Them by Eliminating Internal Toxins! - Video

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Natural Cures For Eczema (Skin Disease) – Video

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Natural Cures For Eczema (Skin Disease)
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All Natural Eczema Treatments – Video

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All Natural Eczema Treatments
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My Review for Fast Psoriasis Cure (2014 watch this review) – Video

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My Review for Fast Psoriasis Cure (2014 watch this review)
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How to Cure Psoriasis – Video

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How to Cure Psoriasis

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Psoriasis Free For Life Review | Is Psoriasis Free For Life All It’s Cracked Up To Be? – Video

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Psoriasis Free For Life Review | Is Psoriasis Free For Life All It #39;s Cracked Up To Be?
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NIH team discovers genetic disorder causing strokes and vascular inflammation in children

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PUBLIC RELEASE DATE:

19-Feb-2014

Contact: Raymond MacDougall macdougallr@mail.nih.gov 301-443-3523 NIH/National Human Genome Research Institute

National Institutes of Health researchers have identified gene variants that cause a rare syndrome of sporadic fevers, skin rashes and recurring strokes, beginning early in childhood. The team's discovery coincides with findings by an Israeli research group that identified an overlapping set of variants of the same gene in patients with a similar type of blood vessel inflammation.

The NIH group first encountered a patient with the syndrome approximately 10 years ago. The patient, then 3 years old, experienced fevers, skin rash and strokes that left her severely disabled. Because there was no history of a similar illness in the family, the NIH group did not at first suspect a genetic cause, and treated the patient with immunosuppressive medication. However, when the NIH team evaluated a second patient with similar symptoms two years agoa child who had experienced recurrent fevers and six strokes by her sixth birthdaythey began to suspect a common genetic cause and embarked on a medical odyssey that has led not only to a diagnosis, but to fundamental new insights into blood vessel disease.

In their study, which appears in the Feb. 19, 2014, advance online edition of the New England Journal of Medicine, the researchers describe how next-generation genome sequencing, only recently available, facilitated a molecular diagnosis for patients in their study. The researchers found that harmful variants in the CECR1 gene impede production of a protein vital to the integrity of healthy blood vessel walls.

"This discovery is another example of genome sequencing playing a central role in revealing the genomic basis for an important rare disease," said Eric D. Green, M.D., Ph.D., director of the National Human Genome Research Institute (NHGRI), where the lead members of the research team are based. "Such studies illustrate how genomics is paving the way to improved human health."

The researchers showed that faulty variants in their patients' DNA that encode the CECR1 gene cause a loss of function of the gene's ability to produce of an enzyme called adenosine deaminase 2 (ADA2). Without it, abnormalities and inflammation in blood vessel walls result. The researchers call the new syndrome, deficiency of ADA2, or DADA2. The enzyme ADA2 is chemically similar to the enzyme ADA1, whose deficiency results in severe combined immunodeficiency disease.

NHGRI Scientific Director Daniel Kastner, M.D., Ph.D., led the team of collaborators from NIH and beyond in mounting the study of nine patients. "It has been incredibly fantastic to see this kind of progress being made within the last decade," he said. "Our study raises the possibility that the ADA2 pathway may contribute to susceptibility to stroke in the more general population."

For children, as with adults, stroke can affect physical, cognitive and emotional functioning. Some outcomes, such as blindness and deafness, can be lasting; others, such as the ability to walk, can be relearned.

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NIH team discovers genetic disorder causing strokes and vascular inflammation in children

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The 10 Biggest Disney Controversies [TOP 10 DISNEY CONTROVERSIES] || MonkeyFacts – Video

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The 10 Biggest Disney Controversies [TOP 10 DISNEY CONTROVERSIES] || MonkeyFacts
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