Researchers achieve human genome analysis at supercomputer speed

While sequencing the human genome in the past has taken many months, researchers recently found a way to analyze 240 full genomes in two days.

A University of Chicago-based team found that genome analysis can be radically accelerated using a supercomputer devoted to life science; their results were in the journal Bioinformatics.

"The supercomputer can process many genomes simultaneously rather than one at a time," first author Megan Puckelwartz, a graduate student involved in the stuy, said in an announcement. "It converts whole genome sequencing, which has primarily been used as a research tool, into something that is immediately valuable for patient care."

Meanwhile, according to study author Elizabeth McNally, Ph.D., the resource can change patient management and eventually add depth to understanding of genetic causes of risk and disease.

The team used raw sequencing data from 61 human genomes and analyzed the data on the supercomputer, using publicly available software packages. They found that shifting to a supercomputer environment improved accuracy and "dramatically" accelerated speed.

Information from these genomes, combined with attention to patient and family histories "adds to our knowledge about these inherited disorders," McNally said. "It can refine the classification of these disorders. By paying close attention to family members with genes that place then at increased risk, but who do not yet show signs of disease, we can investigate early phases of a disorder. In this setting, each patient is a big-data problem."

Better standards are needed for how discoveries in genomic medicine are found and recorded as health information technology develops, according to researchers from Harvard and the Mayo Clinic who published a viewpoint in the Journal of the American Medical Association last spring.

In an interview with FierceHealthIT prior to last year's HIMSS conference in New Orleans, Eric Topol, professor of genomics at The Scripps Research Institute in San Diego, talked about the importance of genome testing for patients. According to Topol, as a society, we're still a long way away from such procedures becoming routine.

"There have only been tens of thousands of people in the world who have had whole genome sequencing," Topol said. "We need millions with various conditions before we know what whole human genome sequences need. We only know of our common variations right now, but most of the important stuff is a low-frequency, rare variance. We know relatively little about that."

To learn more:
- read the announcement from University of Chicago
- check out the study in Bioinformatics

Related Articles:
Researchers call for national standards for genomic data use
Eric Topol: Docs must adopt health IT more quickly
HIMSS13 wrap-up: The news you may have missed
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