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Rady Children’s Hospital-San Diego is expanding the use of whole genome sequencing for critically ill infants, using a demonstration project to show whether the technology can improve clinical outcomes for small babies while cutting care costs.

The effort is empowered by the use of rapid whole genome sequencing (WGS), an accelerated approach that gets sequencing results to clinicians in less than a day. The goal is to improve the accuracy of diagnoses and use that information to change the management of a patient.

Having quick access to this information can have significant results. A patient in a neonatal or pediatric intensive care unit often suffers critical complications or long-lasting side effects that could affect patients the rest of their lives. However, the use of RGS could focus treatment and shorten NICU or PICU stays, reducing both in-hospital and lifetime costs.

The demonstration project, funded by California’s Department of Health, known as Medi-Cal, will look to assess overall costs, and Rady is looking to expand the service to other pediatric health facilities, says Albert Oriol, vice president and CIO for Rady Children’s.

Rady Children’s Hospital

The $2 million state-funded project, called Project Baby Bear, provides genome testing for babies hospitalized in intensive care, leveraging rapid WGS as a first-line diagnostic test done by Rady Children’s Institute for Genomic Medicine for babies at four participating hospitals in the state. The initiative is being led by Stephen Kingsmore, MD, president and CEO of the institute.

At Rady Children’s, rapid WGS orders are placed through the facility’s Epic electronic health records system, and Oriol says the fastest turnaround from order placed to results being available in Epic was just under 20 hours. That compares with three to six weeks for getting results through traditional WGS.

Gaining rapid results can have a huge impact in NICUs or PICUs, where 15 percent to 30 percent of medical issues stem from a genetic cause, Oriol says.

“That helps home in on the specific on the specific issue and how best to manage the patient,” he adds. “One out of every three patients we sequence comes up with a better diagnosis; in 25 percent of these cases, we’ve been able to change the management of the patient; and in one in five, we see a difference in outcomes.”

Before the demonstration project, whole genome sequencing had not been covered by insurance or Medi-Cal; funding was available only through clinical trials paid by research grants or philanthropic donations.

Data from Rady’s Genomic Institute show that nearly 1,200 children had genomic sequencing by last September. Of those, more than one-third received a genomic diagnosis, and physicians were able to adjust care in 70 percent of those cases.

In one case, results of a rapid WGS spared one child from dangerous surgery after the test showed that the surgical procedure would not solve the problem. In another case, a child that was unable to metabolize a nutrient and was experiencing renal failure was diagnosed through genomic sequencing, with the problem solved through administering an inexpensive vitamin.

Oriol says he other payers will cover rapid WGS for pediatric patients if the demonstration project leads Medi-Cal to reimburse for the procedure.
Additionally, Rady’s Genomic Institute aims to expand access to rapid WGS services by building a network of other pediatric healthcare organizations for which it can conduct tests.

“The challenge with rare diseases is that they’re rare,” Oriol says. “We’ve built a network of 15 hospitals that have signed up for the network, and this will allow us to make this diagnostic capability available to other institutions that can’t make the upfront investment for this.

“From an IT standpoint, (Institute president) Kingsmore said we were not going to have the genomics institute become its own ivory tower. It was to be clinically focused, and we needed to interact with (Rady Children’s) very closely,” Oriol continued. “We’ve established a common IT platform—the genomic institute runs on the hospital infrastructure.”

Automating the “entire pipeline” speeds the process, enabling the ability to extract a phenotype, have it analyzed for variants and checking outside databases for known matches of genetic abnormalities. The process also employs artificial intelligence and natural language processing, and there’s future potential to bring automation to the entire process, Oriol says.

“There’s just not enough specialists in this area to go around, and with the use of automation and AI, we can make up for the lack of people and bandwidth,” he concludes.


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