Faced with criticism, electronic health record providers say they are making headway in supporting genomics.

Major providers of electronic health records insist that they are successfully responding to the needs of the emerging field of clinical genomics, despite obstacles including uncertainty over who pays for genomic testing, lack of data standardization and the overall slow pace of change in healthcare.

“We worked closely with our clients, genetic testing labs and standards bodies … to go beyond the PDF report and actually bring discrete genetic testing data into Epic,” said Catherine Prokow, Head of Genomic Products at Epic Systems.

Bob Roebke, vice president of clinical enterprise for Cerner, said the healthcare industry as a whole is still trying to figure out how to incorporate genomics into patient care. Roebke noted that pharmacogenomics hasn’t gotten the distribution he hoped for because providers often have questions about who will pay for testing. “When we start to see this trend, you will see that we are innovating more in [pharmacogenomics],” he said.

There have been some incremental improvements to Cerner’s Millennium EHR core product in recent years, Roebke said. For example, he said that a North Kansas City, Missouri-based firm had responded to customer requests to include physical testing results in the EHR for chart review purposes.

At the American Medical Informatics Association’s (AMIA) November Annual Symposium, Epic and Cerner were the subject of sharp remarks related to their processing of genomic data. To some extent, manufacturers agree with some of the criticisms, but say broader industry collaboration will be needed to provide better support for precision medicine.

In his opening remarks at the AMIA conference in San Diego, Eric Poplar, director and founder of the Scripps Research Institute for Translation, denounced the “computer science duopoly” – although he did not name Epic and Cerner specifically – that does not really get the job done. data clinicians need to practice more precise medicine.

“There is so much data on the homeless,” said Topol, a cardiologist and expert in the integration of genomic and digital technologies. In a subsequent email, he explained that homeless data includes genomics, wearable sensor readings, environmental factors, and other elements that don’t fit into traditional EHR platforms.

Poplar said that the future he described in Dec 2019 Nature Medicine paper about “highly effective medicine,” in which a “digital health trainer” will guide patients to better health, cannot be realized until the EHR has all this ancillary data that will be used by artificial intelligence engines. At AMIA, he expressed the hope that some new entrants, including Graphite Health, Truveta and Tempus, can break the Epic-Cerner duopoly; Poplar is a paid consultant Tempus.

In another AMIA meeting, Nephi Walton, associate medical director for precision genomics at Intermountain Health Care in Salt Lake City, also denounced the technology offered by two of the largest providers of electronic health records.

“We really need a home for genomic data in the EHR,” Walton said. “To obtain [test] the results go to the right place … so they can be used. “

Mizhhirya uses Cerner. Pediatrician Walton previously worked as a clinical genetics specialist for Geisinger Health System in Pennsylvania, a customer of Epic.

Without naming vendors during the AMIA presentation, Walton said getting genomic data from a molecular laboratory at EHR can be quite difficult, although he pointed to the lack of standards more than anything any vendor does.

According to Walton, the key problem is the lack of standardization of genetic phenotypes. This makes it difficult to classify options among patients and reports, with the result that patients with the same options receive different care.

At both Geisinger and Intermountain, Walton has piloted clinical decision support projects based in part on patient genomic data. In both cases, he had to create individual interfaces from EHR to laboratory information systems.

“You have to create an interface for every laboratory you use, and then you have to create a genetic phenotype for every laboratory result you can get,” Walton said in an interview.

The problem of standardization also led vendors to take different approaches to the same problem. Epic is focusing more on public health, Walton said, while Cerner is trying to build on the needs of clinical geneticists. “It would be nice if they could meet in the middle,” he said. In neither case were the needs of leading physicians adequately met.

For their part, manufacturers have acknowledged some of their shortcomings, but said they are making progress.

Roebke said he “would not argue” with Topol or Walton over whether legacy electronic health record providers are innovative in genetics and genomics.

He suggested that Cerner could turn to industry partners for clinical genomics assistance, likely through its Cerner Open Developer Experience (CODE) program. For CODE, the vendor has an app store for add-ons that include genomics apps like 2bPrecise… (Lab and AccessDx software bought 2bPrecise from another major EHR provider, Allscripts Healthcare Solutions, in August.)

Epic, headquartered in Verona, Wisconsin, has created genomics modulethough users have not accepted it universally.

Phil Lindemann, VP of Business Intelligence and Analytics at Epic, has worked on Epic Beaker LIS for ten years. In Lindemann’s early years at the company, the Beaker team “spent a significant amount of time understanding the genetic process and, in fact, the wet lab workflow that would go into that process,” he said.

As genomics evolves, its inclusion of Epic is a shift from single-variant results in LIS to multivariate reporting, cytogenetics and molecular diagnostics, and then, in 2018, to the genomics module in the EHR core. Lindemann said about 90 percent of Epic’s customers are using versions of the EHR software that are less than a year old. The vendor updates their software approximately quarterly.

Lindemann said Epic worked with its clients and major molecular diagnostic laboratories, including Tempus and Foundation Medicine, to figure out how to bring genomic information to the point of care according to standards, including those set by the Global Alliance for Genomics and Health (GA4GH ). … “Laboratories are leading the way in how to interpret and understand genomic information for clinicians, knowing there is this knowledge gap that will need to be closed over time,” he added.

Epic also has dedicated genomics cloud for storing sequences and other large sets of genomic data. “The idea is that this data can be used for research, to make new discoveries, and also be re-interrogated and discovered as knowledge develops,” Prokow said. “Clinically actionable” data can be delivered to the EHR rather than the genomics cloud.

Institutions including University of Pennsylvania, Mayo Clinic, and Arkansas Children’s Hospital have published articles on using Epic to feed structured genetic testing results into clinicians’ workflows for pharmacogenomics and other forms of precision medicine.

Walton, who chairs the AMIA working group on genomics and translational bioinformatics, did say that vendors have made some progress in genomics, but added that the lack of specific standards remains a major obstacle.

Cerner’s Roebke says the standards issue actually presents a great opportunity for vendors to innovate. “I think we have the ability to get this right out of the parachute rather than trying to upgrade as we go forward,” he said.

Cerner has chosen the Health Level Seven International Fast Healthcare Interoperability Resources (FHIR) standard for data transmission. Roebke said the decision puts Cerner “a little behind” because FHIR is not widely used in genomic laboratories. “True or not, we are trying to push the industry towards this,” he said.

Roebke said Cerner could expand quickly if FHIR does gain traction.

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Advised that Epic is actively engaging with standards bodies. Epic is not a corporate member of GA4GH, but Epic’s VP of Genomics and Compatibility Peter DeWolt is personally involved. Epic is also represented on the HL7 Genomics working group.

“Whenever there are places where standards don’t meet requirements or don’t convey the right data, we work with our customers and labs to add and update standards,” through the working groups of the standards organizations, Prokow said.

For example, clients came to Epic looking for a place on the EHR to report mosaicism in genetic test results. “We created a field for this and now we return it to [standards body’s] working group, “Prokow said.

Some concern may arise from the fact that updating standards takes time and that it can also be slow to change organizational culture and work processes as medicine develops.

Walton said he hadn’t heard from any vendor since his AMIA presentation in early November.

Cerner is in the process of selling Oracle for $ 28.3 billion. The public company, whose CEO Neil Patterson died in 2017, has seen a significant change of leadership in recent years. David Feinberg, for whom Walton worked at Geisinger, became CEO of Cerner in October. However, Walton said he currently has no contact with the firm related to genomics and that the beta test of Cerner’s new technology, which was due to begin last summer, remains in limbo.

This story first appeared in our sister publication, Genomeweb

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