By Rob Mitchum // June 28, 2016
Given its expeditionary namesake, it’s only appropriate that Beagle — the University of Chicago’s supercomputer for biomedical research — works with data from all around the world. But a recent project may qualify as the farthest-traveling data yet, as the HPC resource was used in a new genomic study of populations living in the Himalayan mountain range.
Published in Proceedings of the National Academy of Sciences, the study used samples from Himalayan populations as old as 3,150 years ago through modern-day residents of the remote mountain region. As reported by Science Node, the genomes were then shipped to Beagle, which is located at Argonne and operated by staff from the Computation Institute.
Anna Di Rienzo, of the department of human genetics at the University of Chicago, sequenced and analyzed these genomes on the Beagle supercomputer at the Computation Institute and the Tarbell cluster at the Center for Research Informatics. Sequencing and analysis clocked nearly 90,000 processor hours, occasionally using more than 800 processors at a time, she says.
“While ancient DNA work in Europe has made enormous progress and has given new insights into the history of that part of the world, in Asia there is comparatively very little ancient DNA work published,” Di Rienzo points out.
“More than that, the Himalayas and the Tibetan plateau are very interesting in human evolution because: 1) they represent a major barrier to gene flow, and 2) habitation of these regions required major genetic adaptations. Thus ancient DNA can illuminate the history of migration and of adaptations.”
The study also found that the Himalayan populations exhibit high genetic stability over thousands of years, including beneficial mutations for low-oxygen, high-altitude environments. Like this project, further studies blending sample collection in the field and high-performance computing for genomic analysis will likely reveal more about migration and evolution in human populations around the world.