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TGen Adjusting to New Realities of Bioinformatics for Precision Medicine


CHICAGO (GenomeWeb) – The Translational Genomics Research Institute (TGen) became an affiliate of City of Hope National Medical Center in November 2016, with the aim of developing a precision medicine program to detect diseases sooner and improve quality of life and survival for patients.

Duarte, California-based City of Hope was particularly drawn to TGen's expertise in genomic analysis and bioinformatics. Underpinning that know-how is a high-performance computing center at TGen headquarters featuring more than 3,000 processing cores and 3 petabytes of storage.

This affiliation jibes with TGen's primary mission of translating discoveries in the lab into treatments for patients. "It brings us that much closer to the care stream and at scale, whereas before we were doing more boutique kind of work," said CIO James Lowey.

The Phoenix-based research institution actually runs a hybrid cloud environment to handle any spikes in demand for computing power, but most of the data crunching is done in house. "If you have to have a big enough workload and a predictable workload, if you know how to do it, you can generally do it cheaper yourself than you can on Amazon," Lowey said.

In his 16 years with TGen, Lowey has seen — and overseen — plenty of changes in high-performance computing and in biomedical informatics, including during his nine years in charge of HPC. He became CIO in late 2015.

"When I first started, I think there was maybe four or five drugs [for which] that you could actually say, 'Hey, here's the genetic aberration that needs this drug,'" Lowey said. Now, there are more than 60.

"I was originally brought on to build high-performance computers, something near and dear to my heart. And through time, my role has evolved to now be CIO, in charge of all things IT," he recalled. "And what's funny is that now I spend a lot of my time trying to figure out how to get back to spending more time on the computation and the real value-add stuff."

Molecular data volumes have "hockey sticked" with the advent of next-generation sequencing, Lowey said during an interview at last month's Healthcare Information and Management Systems Society (HIMSS) conference in Orlando, Florida.

TGen saw another bump after Illumina came out with its NovaSeq series two years ago, which can generate 8 terabytes of data every 27 hours, prompting an improvement in HPC infrastructure to handle expected future needs.

"Today, we're just not doing the sequencing volume to say we need 10 of these [NovaSeqs]," Lowey said. Still, he has built the infrastructure to handle that kind of data. "I want to change that, and we're working to change that with our partners at City of Hope and some of the others."

TGen freely shares its data with the research community. The affiliation agreement with City of Hope stipulates that the genomics center is free to work with other institutions for the benefit of medicine in general.

TGen appeared at HIMSS as a partner of Dell EMC, the computing infrastructure unit of Dell Technologies. The institution has been working with predecessor companies of Dell EMC since 2009, when TGen installed Isilon high-performance storage technology. The former EMC acquired Isilon in 2010, and then merged with Dell in 2016. The Isilon brand name endures.

Last year, TGen decided to replace its Lustre parallel-based file system for HPC infrastructure with Isilon units that feature flash memory for fast access to data. "We push the Isilon infrastructure ... in particular to its very limits of performance," Lowey said.

TGen was an alpha tester for Isilon F800 all-flash storage nodes after Lowey personally asked Dell Technologies Founder and CEO Michael Dell to be part of the testing.

"The introduction of the flash nodes gave us the performance that was required in order to meet the workload," Lowey recalled. "We ran benchmarks on it and we found that it was running as fast if not faster than our Lustre system," he said. "I don't have a big team, so being able to run as few technology stacks as possible is very desirable."

Informatics is "core" to TGen, but the IT support side is rather small, according to Lowey.

TGen's clinical sequencing arm performs some sequencing for City of Hope and a handful of smaller hospital customers. Since the advent of NovaSeq, the lab has made a full-exome panel the standard.

"Technology has moved on. The idea is to be able to build a system that then we can more rapidly iterate. The thing is, what we're learning through sequencing is guiding what we're doing tomorrow," Lowey said.

Lowey noted that Isilon has native support for the Hadoop Distributed File System, open-source software for managing storage and processing power on commodity hardware, an important consideration when computing needs change often.

He said that Dell EMC has "helped us to move our sequencing and the processing of that sequence data to the next level and we're looking to do it again now. Initially, TGen's motivation for working with Dell EMC technology was a neuroblastoma project, but the City of Hope affiliation has greatly expanded the scope of the organization's work.

Lowey now manages a team of about 25 technologists and works closely with the 50 or so bioinformaticians that the institute has on staff. "We'd rather have scientists. Bioinformatics — we'd rather pay for a bunch of those guys and not as many IT people," he said. IT has become a commodity, but bioinformaticians remain in high demand.

The nature of biomedical research has changed, too. "When I started, lab people came in with white coats and pipettes," Lowey said. "Now, they may have the white coats or they may not, but they're carrying around laptops. Everything has moved into in silico modeling," Lowey said.