The limited ability to analyze multiple genomes simultaneously creates a computational or data bottleneck that increases the time and cost of analysis, limiting the application of next-generation sequencing in the clinical environment. But this spring, researchers from the University of Chicago report adapting a Cray XE6 supercomputer to achieve the parallelization required for concurrent multiple genome analysis. The system, they say, has the capacity to align and call variants on 240 whole genomes in approximately 50 hours. The supercomputer, in combination with publicly available software, not only markedly speeds computational time but also results in increased accuracy and usability of the sequence per genome. Named Beagle, the supercomputer is housed at Argonne National Laboratory outside Chicago. “Improving analysis through both speed and accuracy reduces the price per genome,” said Elizabeth McNally, the director of the Cardiovascular Genetics Clinic at the University of Chicago Medicine in a statement. “With this approach, the price for analyzing an entire genome is less than the cost of 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.” With this computer […]
The limited ability to analyze multiple genomes simultaneously creates a computational or data bottleneck that increases the time and cost of analysis, limiting the application of next-generation sequencing in the clinical environment. But this spring, researchers from the University of Chicago report adapting a Cray XE6 supercomputer to achieve the parallelization required for concurrent multiple genome analysis.
The system, they say, has the capacity to align and call variants on 240 whole genomes in approximately 50 hours. The supercomputer, in combination with publicly available software, not only markedly speeds computational time but also results in increased accuracy and usability of the sequence per genome. Named Beagle, the supercomputer is housed at Argonne National Laboratory outside Chicago.
“Improving analysis through both speed and accuracy reduces the price per genome,” said Elizabeth McNally, the director of the Cardiovascular Genetics Clinic at the University of Chicago Medicine in a statement. “With this approach, the price for analyzing an entire genome is less than the cost of 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.”
With this computer power and price point, the researchers say, it will make it more effective to sequence the entire genome than to order 50 to 70 genes, as McNally does in cardiology practice. For more information on how information technology and software are enabling enhanced clinical use of next-generation sequencing results, please see Inside the Diagnostics Industry on page 5.
