As described on its website, “Rady Children’s Institute for Genomic Medicine was founded as a non-profit organization in 2014 through a transformational pledge of $120 million from Ernest and Evelyn Rady. The Institute is embedded within the 524-bed Rady Children’s Hospital-San Diego, the sixth-largest children’s hospital in the U.S., which contributed $40 million to help establish the Institute. Primary funding for our work—including the genomic sequencing of some patients—comes from philanthropy and grants.”
One leader at Rady Children’s Hospital-San Diego who has been a key member of the team that helped to birth and develop the Rady Children’s Institute for Genomic Medicine has been Albert Oriol, who is vice president of information management and CIO at Rady Children’s Hospital.
On Feb. 4 at the Southern California Healthcare Innovation Summit, which took place at the Hyatt Regency in La Jolla, a suburb of San Diego, and sponsored by Healthcare Innovation, Oriol presented the keynote presentation entitled, “Precision Medicine: Better Care Through IT.” During that presentation, he shared with his audience the story behind the creation and forward evolution of the Rady Children’s Institute for Genomic Medicine, and its success in providing nationwide leadership around leveraging genomic science and medicine to improve children’s health outcomes.
“We happen to be taking care of kids from across the San Diego region: diverse backgrounds, all ethnicities, and very different environments. That gives us a very rich bank of data to pull from,” Oriol told his audience. “In addition, all this data sits on a single instance of our EHR [electronic health record], which encompasses primary care, specialty care, acute care, and post-acute care. In genomics, Southern California is the Silicon Valley of that area—we have tremendous access to experts.”
What’s more, philanthropy played a huge role in the genesis of this organization. “The Institute was started in 2014, based on a tremendous gift from Ernest and Evelyn Rady, who gave us $120 million to establish a genomics institute focused on pediatrics,” Oriol noted. And, he added, “In 2015, Stephen Kingsmore [Stephen Kingsmore, M.D., president and CEO of the Institute] came in to run the genomics institute. We received a grant from the NIH [National Institutes of health] focused on rapid whole genome sequencing in the NICU [nenonatal intensive care unit]. We learned that somewhere between 20 and 30 percent of the kids in the NICU and PICU [pediatric intensive care unit] have a genetic disease that causes or impacts their condition. And we learned that genetic defects are the leading cause of death in the NICU.”
What’s more, Oriol said, “Even though there are 8,000 known genetic defects, many of which are treatable if treated in time, today’s known screenings don’t get us there.” He cited the common example of the infant who is born with a genetic defect connected to his ability to process a particular nutrient. One example might be the inability to process the calcium in his mother’s milk—meaning that every feeding with breastmilk is toxic. “If we don’t know what’s wrong with that baby,” Oriol noted, “we can’t change his course of treatment. And in some cases, we won’t find that out in time. The longer that child goes without a diagnosis, the longer the period of time during which his organs will be damaged by that nutrient that to him is a poison.” Conversely, a correct diagnosis can lead to the appropriate clinical intervention; and all of that relates to the need for early intervention. “Obviously, speed is of the essence.” In addition, 3 percent of children born every year in the U.S. are impacted by a genetic defect, meaning that 70,000 to 80,000 babies born in the U.S. every year could benefit from this work.
Oriol then showed a brief video of Dr. Kingsmore with a mom and with her child, referred to as “Maverick.” The mother explained how Maverick was unable to eat as an infant, and was having constant seizures. As it turned out, Maverick was missing a single protein that creates a single enzyme, and all he needed was treatment with vitamin B6. But normally, the period of time to diagnosis in cases like this one had been weeks, months—even years. In this case, within 36 hours of diagnosis and initial treatment, Maverick was taken off his breathing tube and medications, and is now thriving.
Referring to the video, Oriol told his audience, “The great thing is that if we target the right patient population, making this testing available to them can make a tremendous difference in their quality of life and the care they receive. It also has economic utility,” he underscored. “By being able to quickly identify a diagnosis and get to the adequate treatment, we can get those babies out of a very high-intensity, high-cost setting, and into a lower-cost setting, and have a financial as well as a clinical impact.”
Meanwhile, in terms of the journey, Oriol told the audience, “In 2016, our genomics lab got CLIA-certified, so we went from doing research to taking care of kids in real time. Word got out, and there was tremendous interest from other children’s hospitals. But not every children’s hospital has a Rady family willing to fund this. So as we often do, we partnered with a number of other hospitals; we’re currently working with 26 other children’s hospitals; we’ve become the reference lab for rapid whole-gene sequencing.”
In terms of the mechanics of the process, once a patient is determined to be a good candidate for sequencing, that patient gives consent and is enrolled, and then prepped for the actual sequencing; then the sequencing takes place. “The work involved to support this is incredibly intensive from a computational standpoint, but is relatively automated process,” Oriol explained. “Simultaneously, clinicians go through the patient’s EMR and extract a deep phenotype; this process involves deep phenotype data. Then that data is compared against a number of databases with known genetic data, to determine a diagnosis. So then the clinicians and scientists work to find the right result and determine a course of treatment. It’s very high-tech on the data side, but low-tech on the deep phonotype side, which means it’s not really scalable.” But a solution to that problem was conceived during a meeting in 2018, in which Kingsmore asked whether the team involved could work on automating the process. “And lo and behold, we went ahead and did it,” Oriol said. “We started by rethinking forms, creating smart forms in the NICU; we then brought in natural language processing to really pore over the notes that have this rich, qualitative descriptions in them that really allow us to determine the deep phenotype of the patient. Our physicians think and work in LOINC and HL7 codes, but our scientists think and work in human phenotype ontology. So we really had to marry those two.”
Meanwhile, Oriol said, in automating the process, “The biology side of it stays the same, but the phenotype gets automated. The moment that the physician places the order, the order is sent to a holding warehouse, and once the data points are combined, the magic happens, and we get to a diagnosis. That’s allowed us to move from a manual process that was taking five to six days to less than 20 hours; in the industry, it typically takes six weeks. We can routinely do it in two to three days, sometimes in 20 hours.”
The context of this is important, Oriol noted: “Ten percent of the NICU/PICU admits drive 70 percent of the costs in the acute-care setting”; so the broader impact is potentially huge. Meanwhile, he reported, “We’ve sequenced over 1,000 genomes. We’re working with MediCal, United, and other payers, to prove the utility of these smaller-cohort cases. The outcomes have been impressive, not just because we can do this quickly, but because we can do it accurately. We’re able to get to an actual diagnosis in one of three cases we see. And importantly, that diagnosis drives a change in the management of the patient in one out of four cases; and that leads to improved outcomes in one out of five cases. Doing this takes laser-focused vision,” he added. “We did not try to boil the ocean; we focused on one use case that made sense, where we thought we could have the biggest impact, and we went there.”
Oriol listed several critical success factors that determined how the initiative evolved successfully. They are:
“Check your egos at the door”: the need to focus on mission, not personalities or titles or functions.
A shared vision among the clinicians, scientists, and informaticists.
Keeping an open mind and avoiding conceptual rigidity.
Maintaining a “start-up” mentality, as the need for speed was and has been real.
Focusing on the fact that the work was and is fueling improvements in actual patient care, not just clinical research.
Maintaining processes that ensure patient safety, and accepting the tension between the need for rapid development, and the need to maintain a safe patient care delivery environment and processes.
Partnership along all dimensions has been vital.
“Last but not least, don’t let perfection get in the way of progress. This was evolution over revolution, this was all about making progress from step to step.”
