Using Supercomputers To Speed Up Genome Analysis

February 20, 2014

Image Caption: Beagle, a Cray XE6 supercomputer at Argonne National Laboratory, supports computation, simulation and data analysis for the biomedical research community. Credit: Argonne National Laboratory

Lee Rannals for redOrbit.com Your Universe Online

Researchers writing in the journal Bioinformatics say that genome analysis can be radically accelerated.

Over the years, the cost of sequencing an entire human genome has dropped, but analyzing three billion base pairs of genetic information from a single genome can take months. A team from the University of Chicago is reporting that one of the worlds fastest supercomputers 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, study author Elizabeth McNally, the A. J. Carlson Professor of Medicine and Human Genetics and director of the Cardiovascular Genetics clinic at the University of Chicago Medicine, said in a statement.

Megan Puckelwartz, a graduate student in McNallys laboratory and the studys first author, said the Beagle supercomputer based at Argonne National Laboratory is able to process many genomes simultaneously rather than one at a time.

It converts whole genome sequencing, which has primarily been used as a research tool, into something that is immediately valuable for patient care, Puckelwartz said in a statement.

Scientists have been working on exome sequencing, which focuses on just two percent or less of the genome that codes for proteins. About 86 percent of disease-causing mutations are located in this coding region, but still about 15 percent of significant mutations come from the other coding regions.

Researchers used raw sequencing data from 61 human genomes and analyzed the data on Beagle. They used publicly available software packages and a quarter of the computers total capacity, finding that a supercomputer environment helped with accuracy and speed.

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Using Supercomputers To Speed Up Genome Analysis