GPUs Help Unfold the Loops in Genome’s Graceful Structure

Editor’s note: This is one of a series of five posts profiling finalists for NVIDIA’s 2015 Global Impact Award, which provides $150,000 to researchers using NVIDIA technology for groundbreaking work that addresses social, humanitarian and environmental problems.

Bit by bit, Erez Lieberman Aiden is unfolding the genome.

It’s not easy. Tightly folded inside the nucleus of a cell, the genome is a miraculous physical mechanism for densely storing and rapidly accessing information.

What’s more, he’s doing it in 3D.

Aiden is an assistant professor of genetics at Baylor College of Medicine and of computer science and computational and applied math at Rice University, where he directs the Center of Genome Architecture as well as a CUDA Research Center.

He and a team from Baylor, Rice, MIT, Harvard, and the Broad Institute have used NVIDIA GPUs to map—at the highest resolution to date—how the human genome folds within the nucleus of a cell.

Baylor College of Medicine is among five finalists for NVIDIA’s 2015 Global Impact Award. The annual grant of $150,000 is given to researchers using NVIDIA technology for groundbreaking work addressing social, humanitarian and environmental problems.

An extraordinary computational challenge, the team’s work shed light on the intricate loops of genome architecture. They found the genome regulates its biological function through just a few folds, including the formation of three-dimensional loops.

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The team found the human genome folds into about 10,000 loops, far fewer than were previously suspected. The loops occur when two separate bits of DNA that are far apart come into contact as the genome folds inside a cell’s nucleus.

These loops and other folding patterns in the genome structure form an essential part of gene expression. Just by folding the genome into different shapes, genes switch on or off. This lets cells take on a wide range of functions.

Now, scientists see fine details about genome folding, they are discovering more about a whole new branch of genetic regulation. The maps of looping revealed thousands of hidden switches not known to have existed before. For genes that cause diseases or cancers, locating these switches is essential.

Aiden and the 10-person team, working with NVIDIA Tesla GPUS, created customized algorithms for genomic testing.

“GPUs helped speed up what we do by about 200-fold; doing the same thing on CPUs just wasn’t practical at all,” Aiden said.

“One basic issue is that no one knew what the right algorithm for detecting a loop was. So, we created many variant algorithms, ran them hundreds of times, and compared the results closely,” he said. “This ultimately transformed how we go about annotating loops in the human genome.”

The GPUs help Aiden and his team “to compress time,” he said. “With CPUs it was a week-long process on a single chromosome, and there are 23 chromosomes. But with GPUs we could run our algorithm, grab a coffee, and by the time we were done we could already examine the results. And then we could fix our models, and test again!”

With many diseases linked to genome variation, scientists studying abnormal structures and how these influence changes in the cell can focus on much more detail. Next steps might include examining how particular proteins create certain loops, Aiden said.

For more information on NVIDIA’s Global Impact Award.

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