Using Nvidia GPUs, researchers from Baylor College of Medicine, Rice University, MIT and Harvard University have for the first time mapped how the human genome...
Using Nvidia GPUs, researchers from Baylor College of Medicine, Rice University, MIT and Harvard University have for the first time mapped how the human genome folds in unprecedented detail, a company release showed.
Researchers aided by Nvidia Tesla GPUs – part of the Tesla accelerated computing platform of GPU accelerators and enabling software – just unraveled the genetic “instruction book” that contains about 3 billion base pairs of DNA. That includes all the information needed for our bodies to function, grow, fight off diseases and do millions of other things.
The Japanese word “origami” comes from the words ori, or “folding,” and kami, for “paper.” A skilled artist can turn flat piece of paper into a crane, flower, or a samurai warrior by folding it. Turns out the human genome works in much the same way. Nvidia GPUs aided the researchers to map how the human genome folds in unprecedented detail and capture its “Origami-like” behaviour for the first time.
According to the release, the researchers created the first high-resolution, 3-D maps of entire folded genomes. Among their other discoveries was the fact that the genome works its biological magic with just a few basic folds—including the so-called “3D loop.”
The team, led by former GPU Technology Conference keynote presenter Erez Aiden, assistant professor of genetics at Baylor and of computer science and computational and applied mathematics at Rice, found the human genome is folded into around 10,000 loops. These form when two separate bits of DNA that are far apart come into contact in the folded version of the genome in a cell’s nucleus.
The team soon realised CPUs don’t pack enough power or juice to get the job done and switched to Nvidia, the release claimed. “Ordinary computer CPUs are not well-adapted for the task of loop detection,” said Suhas Rao, a researcher at Baylor’s Center for Genome Architecture. “To find the loops, we had to use GPUs, processors that are typically used for producing computer graphics,” he added.
Miriam Huntley, a doctoral student at Harvard’s school of engineering and applied sciences while talking about the research said, “We faced a real challenge because we were asking, ‘How do each of the millions of pieces of DNA in the database interact with each of the other millions of pieces?Most of the tools that we used for this paper we had to create from scratch because the scale at which these experiments are performed is so unusual.’
This new information might provide new clues for cell function as well as new approaches to combat cancer and other complex diseases.