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Stanford Clinical Genomics Program Nears Launch After Year Delay


CHICAGO (GenomeWeb) – It has taken nearly a year longer than originally planned, but the new, formal Clinical Genomics Program at Stanford Medicine is about a month away from launch.

It is not a coincidence that the launch is tentatively timed for Rare Disease Day, set for Feb. 28 in this non-leap year.

"We have had a vision over the last few years of bringing genomics to the patients of Stanford Health Care," said Euan Ashley, co-director of the Stanford Clinical Genomics Program, director of the Stanford Center for Inherited Cardiovascular Disease, and co-chair of the Stanford Data Science Initiative. "The long-term vision is that this will eventually touch every patient in the healthcare system, but where genomics is right now is in rare disease."

Ashley, a cardiologist, called rare disease "the tip of the spear for genomics into medicine" since exome and genome sequencing have become practically routine in diagnosing and developing treatment plans for difficult-to-diagnose conditions, as well as for hereditary cancers. "It has been, I think, transformative in our ability to diagnose especially children with neurological disorders [and] neurodevelopmental disorders," he added.

Stanford Medical Center happens to be a clinical site for the National Institutes of Health-funded Undiagnosed Diseases Network, and Ashley himself is one of the three principal investigators at this location.

"In the context of undiagnosed disease, we're part of this national network where the NIH has paid for genome and exome sequencing for patients with rare, undiagnosed disease, so we have that process, and [have] seen the benefits of having the physicians who look after the patient very close to the curation and the bioinformatics teams. That's the model for the Stanford service," Ashley said.

Indeed, data is central to the Clinical Genomics Program.

Since 2016, Stanford has been collaborating with Google to develop cloud-based applications for exploring genomic and other healthcare data sets from patients with rare diseases and inherited disorders who are recommended for DNA testing. The two entities agreed to build applications for storing, processing, exploring, and sharing genomic data generated by the Clinical Genomics Program.

Stanford Medicine — particularly Stanford Health Care for adults — has had a lot of turnover in the executive suite in the last year and a half. David Entwistle took over as CEO of Stanford Health Care in July 2016. In 2017, Stanford Health Care got a new chief financial officer, chief operating officer, and chief information officer, and the current chief quality officer has "interim" in her title.

But Ashley said the delay from the planned spring 2017 launch of the Clinical Genomics Program was due to data-related issues rather than leadership changes. Of note, he said, it has taken longer than anticipated to build the program's computing architecture in the Google Cloud.

"A lot of our focus has been thinking about how to deal with high-throughput data within a healthcare system that, other than imaging, has traditionally used very low-throughput data," Ashley said.

"I've been thinking about genomics even as the beginning of high-throughput measurement as it will affect medicine. Eventually, this will include high-throughput metabolomics and potentially proteomics as well," he explained. "We're really building for the next generation, I think, of laboratory healthcare, which is a multi-omic and high-dimensional data world."

Stanford is planning to add bioinformatics staff, but will, at least at the time of the launch, be outsourcing the actual sequencing. "The pipeline and the calling and curating and the sign-out of reports will all be done in-house so it can be done close to the patient and will be done in partnership with the physician who's actually looking out for the patient," Ashley said.

Stanford will tout cooperation between its clinical and bioinformatics teams as a potential competitive advantage. As far as Ashley is concerned, integration is at the heart of clinical genomics.

"We will have this integrated mode where the patient, the physician, the bioinformatics team, the curation team, and the sign-out team are all partners in trying to solve the challenge," he said. At the end of the day, the only point of a diagnostic test is to get the answer" to a patient's diagnosis and treatment.

That, according to Ashley, benefits from multidisciplinary cooperation across the Stanford campus — and not just on the medical side.

"Stanford is known for innovation in technology and computer science," Ashley noted. "A stone's throw away from the hospital are our Department of Engineering and Department of Computer Science, so we have a lot of smart engineers who are very interested in high-throughput biological data [and] genomic data, [and] information theorists and computer scientists who really are thinking for the first time about genomic data. I would hope that we would be able to leverage that expertise to move things rapidly from invention to application in the clinic."

Sometimes that is easier said than done, even within Stanford Medicine. Stanford University Medical Center and the adjacent Lucile Packard Children's Hospital both run Epic Systems electronic health records, but the two hospitals operate independently and implemented their EHRs on different schedules.

An old joke in health IT is that if you've seen one installation of Epic, you've seen one installation of Epic — or any other EHR brand — since each institution has its own workflows and custom tweaks to the software.

"Working between two Epic systems in order to have seamless [genomic test] ordering and reporting happen has not been trivial," Ashley said. "Moving toward the launch has been a big effort from IT, from the pathology side, and from the clinical laboratory."

And now, finally, the Stanford Clinical Genomics Program is just about ready to go.