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Primeur weekly 2014-02-24

Special

H2020: the long road to an integrated open and accessible European e-Infrastructure ...

PRACE, HPC applications and technological development: three ingredients for a top European strategy ...

Yannick Legré is the new director of EGI.eu ...

The Cloud

Red Hat Enteprise Linux OpenStack Platform leveraged by Alcatel-Lucent, CloudBand as part of its Network Functions Virtualization (NFV) Platform ...

AT&T and IBM join forces to deliver new innovations for the Internet of Things ...

Mellanox introduces CloudX Platform to enable companies to build the most efficient public, private and hybrid Clouds ...

EuroFlash

Powerful supercomputer to offer a glimpse of the early universe ...

From a distance: New technique for repair work ...

ECRIN-ERIC to host inauguration ceremony ...

Karlsruhe Institute of Technology to develop ultra-small and ultra–fast electro-optic modulator ...

SURFsara to host Data & Computing Infrastructure Event on 12-13 March 2014 ...

USFlash

SDSC team develops multi-scale simulation software for chemistry research ...

SDSC/UC San Diego researchers hone in on Alzheimer's disease ...

Intel advances next phase of Big Data intelligence: real time analytics ...

Supercomputer dramatically accelerates rapid genome analysis ...

Using computers to speed up drug discovery ...

Better cache management could improve chip performance and cut energy use ...

A step closer to a photonic future ...

HP delivers record-breaking performance and dramatic efficiencies with HP ProLiant servers ...

Researchers propose a better way to make sense of 'Big Data' ...

Mega-bucks from Russia seed development of 'Big Data' tools ...

A new laser for a faster Internet ...

C-DAC to organize Accelerating Biology 2014: Computing Life ...

NetApp introduces unified scale-out storage systems and virtualization software for the unbound Cloud era ...

Supermicro shipping 96 DIMM 4U 4-Way SuperServer featuring new Intel Xeon processor E7-8800/4800 v2 ...

Supercomputer dramatically accelerates rapid genome analysis


20 Feb 2014 Chicago - 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 journalBioinformatics, 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", stated 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", stated first author Megan Puckelwartz, a postdoctoral fellow in Elizabeth 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, Elizabeth 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", Elizabeth McNally stated. "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", stated 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. Elizabeth 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 stated, "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 stated. "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", Elizabeth McNally stated. "It can refine the classification of these disorders", she stated. "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 theHMS 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.
Source: University of Chicago Medicine

Back to Table of contents

Primeur weekly 2014-02-24

Special

H2020: the long road to an integrated open and accessible European e-Infrastructure ...

PRACE, HPC applications and technological development: three ingredients for a top European strategy ...

Yannick Legré is the new director of EGI.eu ...

The Cloud

Red Hat Enteprise Linux OpenStack Platform leveraged by Alcatel-Lucent, CloudBand as part of its Network Functions Virtualization (NFV) Platform ...

AT&T and IBM join forces to deliver new innovations for the Internet of Things ...

Mellanox introduces CloudX Platform to enable companies to build the most efficient public, private and hybrid Clouds ...

EuroFlash

Powerful supercomputer to offer a glimpse of the early universe ...

From a distance: New technique for repair work ...

ECRIN-ERIC to host inauguration ceremony ...

Karlsruhe Institute of Technology to develop ultra-small and ultra–fast electro-optic modulator ...

SURFsara to host Data & Computing Infrastructure Event on 12-13 March 2014 ...

USFlash

SDSC team develops multi-scale simulation software for chemistry research ...

SDSC/UC San Diego researchers hone in on Alzheimer's disease ...

Intel advances next phase of Big Data intelligence: real time analytics ...

Supercomputer dramatically accelerates rapid genome analysis ...

Using computers to speed up drug discovery ...

Better cache management could improve chip performance and cut energy use ...

A step closer to a photonic future ...

HP delivers record-breaking performance and dramatic efficiencies with HP ProLiant servers ...

Researchers propose a better way to make sense of 'Big Data' ...

Mega-bucks from Russia seed development of 'Big Data' tools ...

A new laser for a faster Internet ...

C-DAC to organize Accelerating Biology 2014: Computing Life ...

NetApp introduces unified scale-out storage systems and virtualization software for the unbound Cloud era ...

Supermicro shipping 96 DIMM 4U 4-Way SuperServer featuring new Intel Xeon processor E7-8800/4800 v2 ...