Using Beagle, one of the fastest supercomputers devoted to life sciences, researchers at University of Chicago suggest that the complete genome analysis, involving more than three billion base pairs of genetic information from a single genome, can be radically accelerated, a new study published in the journal Bioinformatics reveals.
"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.