TGen unravels the code of deadly diseases from cancer to COVID-19.

The Translational Genomics Research Institute (TGen^®) is a nonprofit medical research institute affiliated with City of Hope, a world-renowned independent research and treatment center for cancer, diabetes and other life-threatening diseases. TGen’s mission is to perform groundbreaking genetic research to discover more rational, precise and personal treatments for cancer, infectious diseases, neurological disorders and rare childhood disorders.

Through the use of high performance computing (HPC), the institute is able to leverage massive quantities of data to make discoveries and then translate them into treatments quickly and effectively. Data processing speed is an incredibly important concern for TGen researchers because the faster they get results, the faster they can impact, or even save, someone’s life.

James Lowey, TGen CIO, is responsible for making sure his team has the HPC resources they need to secure and manage data and process it quickly and intelligently. Back in 2003, when Lowey first joined TGen, he and his team built a supercomputer with a terabyte file system to process data from the lab’s DNA sequencing microarray. When TGen began working with next-generation sequencing (NGS) in 2008, it took approximately two weeks for the institute’s supercomputer to process an entire genome — an eternity when it comes identifying treatment options for a critically ill patient. According to Lowey, “While microarrays might capture a few thousand genes, NGS can capture your entire genome. You’re talking about 18,000 unique genes and 3 billion base pairs. That created a huge challenge in storing and accessing data generated by these instruments.”

By 2012, the two-week lag time for NGS results had prompted Lowey to reach out to Dell Technologies and Intel^® for assistance with an ambitious HPC project designed to speed up NGS processing times. Both companies made in-kind donations to the project, and engineers from both companies volunteered their time to help create a supercomputer that was optimized to rapidly process NGS samples.

Today, TGen has multiple gene sequencers running around the clock, each one capturing a terabyte or more of data each time it runs. The institute recently upgraded its HPC cluster with new Dell EMC PowerEdge servers, powered by 3,000 Intel Xeon^® cores and with more than three petabytes of Dell EMC Isilon scale-out, network-attached storage. The new system delivers one million CPU hours per month and performs 50 trillion operations per second. Most importantly, the upgraded supercomputer cuts the NGS processing time down to just seven or eight hours.

According to Lowey, “You can have results back the same day, which is huge for patients and their families.” TGen is not resting on its laurels. Lowey and his team are currently working with Dell Technologies and other partners to build a system that can further reduce processing time to just one to two hours.

The supercomputing cluster is also helping TGen in the global fight against COVID-19, helping unravel the mystery of the virus’s DNA. TGen developed an RNA test for COVID-19 and began testing people in March of 2020. TGen researchers are sequencing all the positive test results and building a biobank of genetic signatures to help fight the disease. In addition, other teams are using insights gained from the genetic sequencing to search for drugs that might target the virus.

As part of this effort, TGen accessed the Dell Technologies HPC & AI Innovation Lab in Austin, Texas, to analyze data on the lab’s Zenith supercomputer. “We took a pretty good subset of all the known sequences of COVID, loaded it into the supercomputer and ran some very complex analysis of that,” Lowey says. “This work helped us come up with a possible drug-able target that was reflected in the genome of the virus.”

As the field of genomics continues to evolve at a rapid pace, TGen needs partners who help solve problems. According to Lowey, “That requires a company who has both the products and the brains to work with us to come up with a solution to a very hard problem…Technology is important. You have to have that. You have to have great tools to do the job. But you also have some alignment on what you’re trying to accomplish…Having a partner who is truly invested in trying to change things for the better is absolutely critical. That’s something we value immensely.”

Read the case study: Groundbreaking research with life-changing results. Learn more about TGen,with Dell Technologies and Intel.