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Nationwide Children's Hospital Integrating Genomics Into Clinical Care


CHICAGO (GenomeWeb) – Even before the official launch of its Institute for Genomic Medicine in the fall of 2016, Nationwide Children's Hospital in Columbus, Ohio, had designs on fusing genomics with traditional clinical care as seamlessly as possible.

"[Genomics] just becomes part of the mechanism for generating evidence towards diagnosis and treatment decisions," said Elaine Mardis, the institute's co-executive director. "That's the way that we view it, as just a piece of the evidence puzzle, if you will, that a clinician needs to put together to figure out the best treatment for that patient on an individualized basis."

Nationwide recruited Mardis and Executive Director Richard Wilson from Washington University in St. Louis in 2016 to establish the Institute for Genomic Medicine. At Wash U, they led the McDonnell Genome Institute, one of the four original genomics centers in the US funded by the National Human Genome Research Institute.

The two brought their experience in next-generation sequencing to Ohio's capital, where they helped create genomic pipelines and implement related technologies.

"Mainly, what we're trying to do is facilitate clinical translation of things that we originally have learned in the research space," Wilson explained. "That [means] utilization of not only discoveries from cancer and other samples, but also how to migrate some of the tools, applications, laboratory methods, and software tools and pipelines from the research space to the clinical space," Wilson said.

"The institute that we launched here just over a year ago does both traditional genomics research and we also have the cytogenetics and molecular genetics clinical testing lab," Wilson said.

From the start, there was a plan for a controlled rollout. "The problem is that we have more people who are interested than we can manage in terms of different specialties and the different types of patients that we see here," Mardis said.

"The way we view the opportunity here is that you're seeing [next-generation sequencing]-based diagnostics applied in adults really predominantly in the cancer setting, whereas in pediatrics, there are multiple places where this can be inserted into the standard workup for diagnostic measures. There are more opportunities to do more, I think."

When the Institute for Genomic Medicine opened, the first order of business was to create the computing infrastructure to support precision medicine. Mardis said that the hospital was able to do this by supplementing existing IT systems with Amazon Web Services.

"We had a pretty good understanding of what it was going to take computationally," Wilson said. "One of the things we were able to do when we came here was to do a lot of the genome computing in the cloud."

This helped the Institute for Genomic Medicine determine that it was possible to perform large-scale exome sequencing for many patients and whole-genome sequencing for certain cancer patients. "That's a protocol that we're currently trying to roll out," Wilson said.

"[The cloud] supplants the need to build a big data center, which is what we did at Wash U," Mardis said. Wash U was the first to sequence whole genomes for cancer, in 2008, even before exome capture came along, she noted.

"At the time we did it, that was the only option, but now there are other options. The cloud environment is becoming a bit more cost-competitive as well because there are multiple clouds that one can compute in," she explained. Plus, bandwidth limitations are minimal with smart data management.  

"As the data come off of the Illumina sequencing machines, they go through our data pipe up to the Amazon cloud. The alignment and remaining compute to identify variants happens there, and we pull the data back down," Mardis said.

"We're committed to doing some whole-genome work. As long as you're just taking the data packets as they come off of the sequencer and not waiting until the run is completed and trying to shove it all through the pipe at once, it's much more manageable," Mardis said.

Nationwide initially launched whole-exome testing for congenital defects, and the cancer protocol is being rolled out as 2018 starts. "Our next target is going to be epilepsy," Mardis said.

Nationwide Children's, one of America's largest pediatric hospitals, has already made whole-exome sequencing an insurance-billable lab test, taking advantage of the fact that many insurance plans, including Medicaid, do cover exome testing.

"You see a lot of kids who come here with obvious genetic disease, and now we're able to whole-exome sequencing for the patients and their parents and sometimes unaffected siblings to improve the chances of getting those families a molecular diagnosis," Wilson said.

"The basic idea is that you have for the exome sequencing a clinician who's identifying a child that might be able to benefit from this type of germline evaluation," Mardis explained. In cancer, an oncologist or surgeon who sees a patient with a poor prognosis or a rare subtype without an established care standard should be able to order genetic testing in hopes of finding experimental therapies or clinical trials, she added.

The goal is for clinicians to view sequencing as just another tool for them to turn to, according to Mardis. "If it does become more acceptable and provides more precision, on a patient-by-patient basis, we hope to build the confidence of our clinicians in including this as part of the standard of care, in terms of the diagnostic workup," she explained.

"I can't say that we're there yet for every patient, but there's also this need to support the clinical benefit that these kinds of data bring to the patients individually in terms of outcomes before it really becomes the de facto standard-of-care diagnostic workup," Mardis continued. "There's a little bit of legwork to be done in terms of supporting clinical benefit, which is why we're doing this in a sort of prototype approach initially. Over time, it may become more integrated, more de rigeur."