By Allison Proffitt

November 20, 2015 | It’s been a busy year for Howard Jacob. In March, he and several members of his team decided to leave the Medical College of Wisconsin in Milwaukee for positions in Huntsville, Alabama. The HudsonAlpha Institute announced his appointment as Executive Vice President for Medical Genomics and Chief Medical Genomics Officer on April 7. And when I visited his new office in late August, he was planning a November 1 clinic opening.

“People have been running pretty hard and pretty fast,” Jacob said in August. “I think it’s awesome! I’m not sure everybody else is quite happy with it yet, but ultimately they will be.”

Jacob didn’t quite make his November 1 deadline, but today HudsonAlpha held the grand opening for the Smith Family Clinic for Genomic Medicine, a collaboration between the HudsonAlpha Institute, the University of Alabama at Birmingham; and Children's of Alabama, a pediatric medical center.

The Smith Family Clinic is named in honor of the Mark C. Smith family, an entrepreneurial Huntsville family whose support has made it possible to bring genomic medicine to Huntsville.

The starting point for the Smith Family Clinic will be rare diseases—“[Rare] is a horrible name,” Jacob said. “There’s 20 million Americans with an undiagnosed disease. That’s 5% of the population. So every time you’re in a room for 20 people, there’s somebody impacted by rare disease.”

But the challenges before the Smith Family Clinic and genomic medicine are anything but rare.

Clinicians want to know if a molecular diagnosis will actually change clinical care, especially for patients who already have a diagnosis, Jacob said. “But how often are they right with that diagnosis? Versus how often is it something that looks similar to the diagnosis?” Jacob asked. “[Clinicians] will tell you firsthand, sometimes they just miss it! It will look like some particular disease, but it turns out that’s not it at all.”

Jacob hopes that the clinic will help facilitate a broad view of clinical utility: not just how a molecular diagnosis could heal or fix one patient, but how truly accurate diagnoses can inform the patient’s treatment decisions, help the patient’s family, and add to our understanding of what genes do, he explained.

He also hopes for a revolution in clinical trials. “The clinical trial system is designed for average. It is not designed for the individual,” he said. “The bad news about this is we’re also making mistakes when it comes to common disease also. Common disease doesn’t mean it’s caused by the same thing; common disease means we have similar clinical phenotype.”

The trick, then, is to, “take basic research and pre-position it so that when we find a variant of uncertain significance we can test it at the speed of the clinic.”

Building a Clinic

“It’s an absurd statement: doing basic research at the speed of the clinic,” Jacob conceded. But that’s his goal for HudsonAlpha.

Leading the push at the Smith Family Clinic is David Bick, one of the team from Medical College of Wisconsin in Milwaukee that joined HudsonAlpha earlier this year. Bick serves as Medical Director of the Smith Family Clinic for Genomic Medicine. He’s Board-certified in pediatrics, clinical genetics, and clinical molecular genetics, and said that HudsonAlpha is the ideal situation for perusing genomic medicine.  

“We really do believe that genomics is going to change the practice of medicine, and we are setting up the clinic basically with that in mind,” he told Clinical Informatics News last week.

The Smith Family Clinic plans to use exclusively whole genome sequencing, Bick said, in caring for patients with rare diseases. The space is built for patients with serious medical issues, Bick said. Wide hallways and doorways make it easy for patients to move through the building.

An online patient portal has been designed to collect as much information as possible from the patient and apply it to the diagnostic pipeline, making the analysis process smoother for both the patients and their physicians, Bick said. Patient families can input medical history, phenotype details, and treatment history from home, at their leisure, before their appointments. They can access a library of videos that explain whole genome sequencing, incidental findings, and what sequencing can and cannot reveal.  

Diligently collecting phenotype details can make all the difference in diagnosis, Bick said. “For those cases where I have a very rich phenotype, my probability of finding answers goes up.”

Medical history, clinical observations, and phenotype will be combined with whole genome sequencing and HudsonAlpha’s own genomic analysis pipelines. Patients will be sequenced in HudsonAlpha’s genome center on the Illumina X10 platform, and sequence analysis will be done with pipelines developed by Liz Worthey and her team, another Wisconsin transplant. Worthey developed the clinical genomics pipeline that helped pioneer rare disease genomics several years ago when treating Nick Volker.

The Business of Genomics

Each of these pieces is important—a thoughtful clinic experience for patients and their families, best practices in sequencing, and accurate genome analysis—and Bick hopes to truly distinguish the Smith Family Clinic by doing it affordably at scale.

“What we’re trying to achieve is combining excellence in the laboratory—doing the actual sequencing itself, excellence in informatics—and our own clinical work to make the whole process be the best that it could be for that patient, to ensure that the most information is used for analyzing that genome.”

In support of that, the clinic is investing in telemedicine. “Just like we believe genomics is going to change the practice of medicine, telemedicine is also changing the way physicians practice.”

Bick said that for patients outside of northern Alabama, families can visit a local physician’s office and have a concurrent telemedicine visit with the Smith Family Clinic. “We can have a telemedicine visit with them. We can explain genomics, we can discuss their child’s care. I can do the external physical exam and the local physician can put his stethoscope on the child’s chest [for example],” he explained.  

Another part of the solution, Bick believes, is automating data handling for better analysis, and a better patient experience. “From the moment that a physician and their patient decide that, ‘Wow, I think a genome might be helpful,’ to the very end where we’re providing an answer—that whole pipeline—we have to reduce the cost of that.”

Bick said the initial goal is to provide a diagnosis three months after a patient contacts the clinic. Patient portals and informative counseling videos will help reduce costs and increase ease for patients and physicians during intake, Bick said.  

“If you can move clinical information out of the portal, out of the medical record, and into the laboratory in a structured way, then that structured information can be combined with the sequence data [for analysis],” he added.  

Genomics will, “only change the practice of medicine if we can reduce the cost of the entire process from the time that the physician and the patient think about it all the way through the counseling, the genetics visit, looking for changes, the reporting, and explaining it back,” Bick said. “We have to reduce the cost of that whole thing and make it a better experience for the patient and the physician, otherwise it’s not going to be used in medicine.”

EDITOR’S NOTE: Howard Jacob will be one of the plenary speakers at the 2016 Bio-IT World Conference & Expo in Boston, April 5-7, 2016. Registration is open now.