The completion of the Human Genome Project in 2000 was heralded by its leaders as a landmark event not just for biology, but for the practice of medicine as well. But 14 years later, few applications of genomics have made their way from the laboratory to the clinic. In a story for Reuters, reporter Julie Steenhuysen takes a look at some early signs that the promise of genomic medicine may finally be realized -- for a few diseases, at least. While science entrepreneur Craig Venter grabs headlines with his new Human Longevity company, Steenhuysen also credits ground-breaking work on the CI's Beagle supercomputer for breaking down some of the data and computational obstacles that have slowed the use of genomics in the clinic.
Among the researchers featured in the story is Elizabeth McNally, director of the Cardiovascular Genetics Clinic at the University of Chicago Medicine. Through sequencing 60 to 70 genes from patients with a family history of cardiovascular conditions, McNally is able to make more specific diagnoses and change patient treatment plans with a specificity that would not have been possible before clinical genetic methods. But the future is even more exciting, as McNally's group works with Lorenzo Pesce and the Beagle team to streamline the sequencing of whole genomes instead of just a handful of representatives, loosening one of the key bottlenecks that have choked clinical applications.
Although McNally uses panels of 70 to 80 genes in her clinic, she has started experimenting with whole genomes. With the reduced cost of gene mapping, whole gene sequencing is a potentially cheaper, more powerful tool.
The reduced cost of mapping is cutting the cost of research, too -- another factor that could speed clinical outcomes. McNally's team recently published a paper in the journal Bioinformatics in which she used Beagle, a supercomputer housed at Argonne National Laboratory, to analyze 240 full genomes in about two days. Such an endeavor normally takes months.
"That dramatically decreases the cost associated with analysis because we sped up the time," said McNally.
You can read more about the Beagle's rapid genome analysis acceleration at the University of Chicago Medicine newsroom, and from the original journal article in Bioinformatics.