Roadrunner Supercomputer Employed In HIV Evolutionary Tree For Vaccine Use

October 27, 2009 5:35 p.m. EST

Los Alamos, NM (AHN) - Researchers are using the Roadrunner supercomputer to analyze vast quantities of genetic sequences from HIV infected people in the hope of zeroing in on possible vaccine target areas.

It is the hope of scientists that Physicist Tanmoy Bhattacharya and HIV researcher Bette Korber used samples across the globe - from both chronic and acute HIV patients - and created an evolutionary genetic family tree, known as a phylogenetic tree, to look for similarities in the acute versus chronic sequences that may identify areas where vaccines would be most effective.

During this study researchers were able to analyze and compare the evolutionary history of more than 10,000 sequences from more than 400 HIV-infected individuals. Korber and his colleagues are hoping to identify common features of the transmitted virus, and attempt to create a vaccine that enables recognition of the original transmitted virus before the body's immune response causes the virus to react and mutate.

"DNA Sequencing technology, however, is currently being revolutionized, and we are at the cusp of being able to obtain more than 100,000 viral sequences from a single person," said Korber. "For this new kind data to be useful, computational advances will have to keep pace with the experimental, and the current study begins to move us into this new era."

The supercomputer gives researchers the capacity to look for similarities across whole populations of acute patients.

Bhattacharya continues, "At this scale we can begin to figure out the relationships between chronic and acute infections using statistics to determine the interconnecting branches - and it is these interconnections where a specially-designed vaccine might be most effective.

The IBM designed Roadrunner supercomputer is capable of performing 1 million billion calculations per second.