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Whole genome analysis, stat
Date:2/19/2014

e 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
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Contact: John Easton
john.easton@uchospitals.edu
773-795-5225
University of Chicago Medical Center
Source:Eurekalert  

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