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Credit: NIGMS
The time needed to sequence an entire human genome has decreased greatly in recent years, but analyzing the resulting 3 billion base pairs of genetic information from a single genome can take many months.
Now, researchers have found they can accelerate whole-genome analysis using a Cray XE6 supercomputer.
The team found this computer could process many genomes at once and was able to analyze 240 full genomes in a little over 2 days.
The researchers reported these results in Bioinformatics.
The team used Beagle, a Cray XE6 supercomputer located at Argonne National Laboratory in Illinois, in an attempt to analyze multiple genomes concurrently.
Using publicly available software packages and one quarter of its total capacity, the computer was able to align and call variants on 240 whole genomes in approximately 50 hours.
But the computer did not only speed up whole-genome analysis. It also increased the usable sequences per genome.
“Improving analysis through both speed and accuracy reduces the price per genome,” said study author Elizabeth McNally, MD, PhD, of the University of Chicago.
“With this approach, the price for analyzing an entire genome is less than the cost of looking at just a fraction of the genome. New technology promises to bring the costs of sequencing down to around $1000 per genome. Our goal is get the cost of analysis down into that range.”
The findings of this research have immediate medical applications, according to Dr McNally. She noted that she and her colleagues must often sequence genes from an initial patient as well as multiple family members in order to better understand and either treat or prevent a disease.
“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.”
Furthermore, the range of testable mutations has greatly increased in recent years.
“In the early days, we would test 1 to 3 genes,” Dr McNally said. “In 2007, we did our first 5-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 inherited disorders, according to Dr McNally.
“It can refine the classification of these disorders,” she said. “By paying close attention to family members with genes that place them at increased risk, but who do not yet show signs of disease, we can investigate early phases of a disorder.” 
Credit: NIGMS
The time needed to sequence an entire human genome has decreased greatly in recent years, but analyzing the resulting 3 billion base pairs of genetic information from a single genome can take many months.
Now, researchers have found they can accelerate whole-genome analysis using a Cray XE6 supercomputer.
The team found this computer could process many genomes at once and was able to analyze 240 full genomes in a little over 2 days.
The researchers reported these results in Bioinformatics.
The team used Beagle, a Cray XE6 supercomputer located at Argonne National Laboratory in Illinois, in an attempt to analyze multiple genomes concurrently.
Using publicly available software packages and one quarter of its total capacity, the computer was able to align and call variants on 240 whole genomes in approximately 50 hours.
But the computer did not only speed up whole-genome analysis. It also increased the usable sequences per genome.
“Improving analysis through both speed and accuracy reduces the price per genome,” said study author Elizabeth McNally, MD, PhD, of the University of Chicago.
“With this approach, the price for analyzing an entire genome is less than the cost of looking at just a fraction of the genome. New technology promises to bring the costs of sequencing down to around $1000 per genome. Our goal is get the cost of analysis down into that range.”
The findings of this research have immediate medical applications, according to Dr McNally. She noted that she and her colleagues must often sequence genes from an initial patient as well as multiple family members in order to better understand and either treat or prevent a disease.
“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.”
Furthermore, the range of testable mutations has greatly increased in recent years.
“In the early days, we would test 1 to 3 genes,” Dr McNally said. “In 2007, we did our first 5-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 inherited disorders, according to Dr McNally.
“It can refine the classification of these disorders,” she said. “By paying close attention to family members with genes that place them at increased risk, but who do not yet show signs of disease, we can investigate early phases of a disorder.”
Credit: NIGMS
The time needed to sequence an entire human genome has decreased greatly in recent years, but analyzing the resulting 3 billion base pairs of genetic information from a single genome can take many months.
Now, researchers have found they can accelerate whole-genome analysis using a Cray XE6 supercomputer.
The team found this computer could process many genomes at once and was able to analyze 240 full genomes in a little over 2 days.
The researchers reported these results in Bioinformatics.
The team used Beagle, a Cray XE6 supercomputer located at Argonne National Laboratory in Illinois, in an attempt to analyze multiple genomes concurrently.
Using publicly available software packages and one quarter of its total capacity, the computer was able to align and call variants on 240 whole genomes in approximately 50 hours.
But the computer did not only speed up whole-genome analysis. It also increased the usable sequences per genome.
“Improving analysis through both speed and accuracy reduces the price per genome,” said study author Elizabeth McNally, MD, PhD, of the University of Chicago.
“With this approach, the price for analyzing an entire genome is less than the cost of looking at just a fraction of the genome. New technology promises to bring the costs of sequencing down to around $1000 per genome. Our goal is get the cost of analysis down into that range.”
The findings of this research have immediate medical applications, according to Dr McNally. She noted that she and her colleagues must often sequence genes from an initial patient as well as multiple family members in order to better understand and either treat or prevent a disease.
“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.”
Furthermore, the range of testable mutations has greatly increased in recent years.
“In the early days, we would test 1 to 3 genes,” Dr McNally said. “In 2007, we did our first 5-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 inherited disorders, according to Dr McNally.
“It can refine the classification of these disorders,” she said. “By paying close attention to family members with genes that place them at increased risk, but who do not yet show signs of disease, we can investigate early phases of a disorder.”