Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Whole genome analysis, stat

20.02.2014
Supercomputer dramatically accelerates rapid genome analysis

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.


Beagle, a Cray XE6 supercomputer at Argonne National Laboratory, supports computation, simulation and data analysis for the biomedical research community.

Credit: Argonne National Laboratory

In the journal Bioinformatics, however, a University of Chicago-based team—working with Beagle, one of the world's fastest supercomputers devoted to life sciences—reports 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 McNally's 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, McNally's 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 computer's 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."

The finding has immediate medical applications. McNally's Cardiovascular Genetics clinic, for example, relies on rigorous interrogation of the genes from an initial patient as well as multiple family members to understand, treat and prevent disease. More than 50 genes can contribute to cardiomyopathy. Other genes can trigger heart failure, rhythm disorders or vascular problems.

"We start genetic testing with the patient," she said, "but when we find a significant mutation we have to think about testing the whole family to identify individuals at risk."

The range of testable mutations has radically expanded. "In the early days we would test one to three genes," she said. "In 2007, we did our first five-gene panel. Now we order 50 to 70 genes at a time, which usually gets us an answer. At that point, it can be more useful and less expensive to sequence the whole genome."

The information from these genomes combined with careful attention to patient and family histories "adds to our knowledge about these inherited disorders," McNally said. "It can refine the classification of these disorders," she said. "By paying close attention to family members with genes that place then at increased risk, but who do not yet show signs of disease, we can investigate early phases of a disorder. In this setting, each patient is a big-data problem."

Beagle, a Cray XE6 supercomputer housed in the Theory and Computing Sciences (TCS) building at Argonne National Laboratory, supports computation, simulation and data analysis for the biomedical research community. It is available for use by University of Chicago researchers, their collaborators and "other meritorious investigators." It was named after the HMS Beagle, the ship that carried Charles Darwin on his famous scientific voyage in 1831.

The National Institutes of Health and the Doris Duke Charitable Foundation funded this study. Additional authors include Lorenzo Pesce, Viswateja Nelakuditi, Lisa Dellefave-Castillo and Jessica Golbus of the University of Chicago; Sharlene Day of the University of Michigan; Thomas Coppola of the University of Pennsylvania; and Gerald Dorn of Washington University.

John Easton | EurekAlert!
Further information:
http://www.uchospitals.edu

More articles from Life Sciences:

nachricht New switch decides between genome repair and death of cells
27.09.2016 | University of Cologne - Universität zu Köln

nachricht A blue stoplight to prevent runaway photosynthesis
27.09.2016 | National Institute for Basic Biology

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: First quantum photonic circuit with electrically driven light source

Optical quantum computers can revolutionize computer technology. A team of researchers led by scientists from Münster University and KIT now succeeded in putting a quantum optical experimental set-up onto a chip. In doing so, they have met one of the requirements for making it possible to use photonic circuits for optical quantum computers.

Optical quantum computers are what people are pinning their hopes on for tomorrow’s computer technology – whether for tap-proof data encryption, ultrafast...

Im Focus: OLED microdisplays in data glasses for improved human-machine interaction

The Fraunhofer Institute for Organic Electronics, Electron Beam and Plasma Technology FEP has been developing various applications for OLED microdisplays based on organic semiconductors. By integrating the capabilities of an image sensor directly into the microdisplay, eye movements can be recorded by the smart glasses and utilized for guidance and control functions, as one example. The new design will be debuted at Augmented World Expo Europe (AWE) in Berlin at Booth B25, October 18th – 19th.

“Augmented-reality” and “wearables” have become terms we encounter almost daily. Both can make daily life a little simpler and provide valuable assistance for...

Im Focus: Artificial Intelligence Helps in the Discovery of New Materials

With the help of artificial intelligence, chemists from the University of Basel in Switzerland have computed the characteristics of about two million crystals made up of four chemical elements. The researchers were able to identify 90 previously unknown thermodynamically stable crystals that can be regarded as new materials. They report on their findings in the scientific journal Physical Review Letters.

Elpasolite is a glassy, transparent, shiny and soft mineral with a cubic crystal structure. First discovered in El Paso County (Colorado, USA), it can also be...

Im Focus: Complex hardmetal tools out of the 3D printer

For the first time, Fraunhofer IKTS shows additively manufactured hardmetal tools at WorldPM 2016 in Hamburg. Mechanical, chemical as well as a high heat resistance and extreme hardness are required from tools that are used in mechanical and automotive engineering or in plastics and building materials industry. Researchers at the Fraunhofer Institute for Ceramic Technologies and Systems IKTS in Dresden managed the production of complex hardmetal tools via 3D printing in a quality that are in no way inferior to conventionally produced high-performance tools.

Fraunhofer IKTS counts decades of proven expertise in the development of hardmetals. To date, reliable cutting, drilling, pressing and stamping tools made of...

Im Focus: Launch of New Industry Working Group for Process Control in Laser Material Processing

At AKL’16, the International Laser Technology Congress held in May this year, interest in the topic of process control was greater than expected. Appropriately, the event was also used to launch the Industry Working Group for Process Control in Laser Material Processing. The group provides a forum for representatives from industry and research to initiate pre-competitive projects and discuss issues such as standards, potential cost savings and feasibility.

In the age of industry 4.0, laser technology is firmly established within manufacturing. A wide variety of laser techniques – from USP ablation and additive...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

Laser use for neurosurgery and biofabrication - LaserForum 2016 focuses on medical technology

27.09.2016 | Event News

Experts from industry and academia discuss the future mobile telecommunications standard 5G

23.09.2016 | Event News

ICPE in Graz for the seventh time

20.09.2016 | Event News

 
Latest News

New switch decides between genome repair and death of cells

27.09.2016 | Life Sciences

Nanotechnology for energy materials: Electrodes like leaf veins

27.09.2016 | Physics and Astronomy

‘Missing link’ found in the development of bioelectronic medicines

27.09.2016 | Life Sciences

VideoLinks
B2B-VideoLinks
More VideoLinks >>>