Using the Power of HPC to Save Lives
- November 19, 2020
Dell Technologies and the Translational Genomics Research Institute (TGen) have a long history of collaborating to enable groundbreaking research with life-changing results. Located in Phoenix Arizona, TGen is a nonprofit medical research institute affiliated with City of Hope, a world-renowned independent research and treatment center for life-threatening diseases.
TGen leverages multiple Dell Technologies supercomputers to unravel the secrets of the human genome and develop precision medicines for diseases such as COVID and other infectious diseases, cancer, neurological disorders, and rare childhood disorders. TGen uses its supercomputing power to identify more precise and personal treatment options, sooner, to save more lives.
For example, TGen is already running an HPC cluster used primarily for pathogen genomics and is in the process of building a newer system based on Dell EMC PowerEdge R640 Servers with Intel® Xeon® Scalable processors, Dell EMC Isilon storage and Dell EMC PowerSwitch networking.
TGen and City of Hope also have a GPU-centric system based on Dell EMC PowerEdge C4140 and R640 Servers with NVIDIA® V100 GPUs, Dell EMC PowerSwitch networking and Dell EMC Isilon network attached storage that they use primarily for molecular dynamics simulations.
Now, an upgraded HPC system, originally built by TGen, Dell Technologies and Intel in 2012, is enabling TGen to handle the massive quantities of data involved in genome sequencing. Building the system was no small engineering feat, because next-generation sequencing (NGS) typically captures a terabyte or more of data each time a sequencer runs, and TGen runs multiple sequencers run around the clock. TGen needed an HPC system capable of storing, processing and computing against those massive data sets—with a goal of dramatically reducing time to results.
The upgraded supercomputer gives TGen the processing power of 3,000 Intel® Xeon® processing cores, giving researchers 1 million CPU hours per month to perform 50 trillion operations per second. The genomics sequencing system also offers more than 3 petabytes of Dell EMC Isilon scale-out network-attached storage.
The upgrade cuts the data processing time from two weeks to just eight hours. This dramatic performance improvement enables TGen to deliver personalized treatments that save lives, sooner. It’s also helping TGen unravel the secrets of infectious diseases, which are also DNA-based organisms. That’s helping the institute take an active role in the fight against COVID-19. TGen has developed an RNA test for COVID-19 and has been testing local patients since March 2020. The researchers are sequencing all of the positive test results and building a biobank of genetic signatures for the disease over time.
Researchers at TGen can then use the insights gained from sequencing the virus to search for drugs that might be effective against it. As part of this project, TGen can analyze data on the Dell Technologies HPC & AI Innovation Lab’s Zenith supercomputer. As an affiliate of City of Hope, TGen is contributing to the preclinical development of a vaccine for the novel coronavirus.
According to TGen CIO James Lowey, “Over a number of years, I’ve had the opportunity to work with many people at Dell who are really passionate about what they do and believe in the mission. I think Michael Dell puts it best when he says it’s not just about building technology for technology’s sake. It’s about building technology to solve problems, to work in the real work and to make a difference. That philosophy aligns very closely with what we are trying to do here at TGen. Having a partner who is truly invested in trying to change things for the better is absolutely critical. That’s something we value immensely.”
A new case study outlines the long relationship between TGen and Dell Technologies, as well as the technical details and astounding results of the recent NGS system upgrade and its impact on COVID-19 research.