Facing criticism, electronic health records vendors say they’re making progress in supporting genomics

Major electronic health records vendors insist they are successfully responding to the needs of the emerging field of clinical genomics, despite barriers including uncertainly about who pays for genomic testing, lack of data standardization, and the general slow pace of change in healthcare.

“We’ve worked closely with our customers, with genetic testing labs, and standards bodies … to go beyond the PDF results report and actually bring discrete genetic testing data into Epic,” said Catherine Procknow, genomics product lead at Epic Systems.

Bob Robke, VP of clinical enterprise at Cerner, said that the healthcare industry in general is still struggling to understand how to incorporate genomics into patient care. Robke noted that pharmacogenomics has not had the uptake he had hoped because providers frequently have issues regarding who will pay for testing. “When we start seeing that trend move, you’ll see us doing more innovation in [pharmacogenomics],” he said.

There have been some incremental improvements to the core Cerner Millennium EHR product in recent years, according to Robke. For example, he said that the North Kansas City, Missouri-based firm has responded to client requests to include somatic testing results in the EHR for chart review purposes.

Epic and Cerner were the target of some pointed barbs at November’s American Medical Informatics Association (AMIA) Annual Symposium related to their handling of genomic data. To a degree, the vendors agree with some of the criticisms, but say that it will take wider industry cooperation to provide better support for precision medicine.

In his opening keynote address to the AMIA conference in San Diego, Eric Topol, director and founder of the Scripps Research Translational Institute, decried a “duopoly of informatics” —though he did not specifically name Epic and Cerner — that does not properly deliver all the data clinicians need to practice more accurate medicine.

“There is so much homeless data out there,” said Topol, a cardiologist and an expert on the integration of genomic and digital technologies. In a subsequent email, he explained that “homeless” data includes genomics, readings from wearable sensors, environmental factors, and other items that do not fit neatly into traditional EHR platforms.

Topol said that a future that he described in a 2019 Nature Medicine paper about “high-performance medicine” in which a “digital heath coach” would guide patients toward better health could not be realized until EHRs have all of this adjunct data to feed artificial intelligence engines. At AMIA, he expressed hope that some newer entrants including Graphite Health, Truveta, and Tempus might break the Epic-Cerner duopoly; Topol is a paid consultant to Tempus.  

In another AMIA session, Nephi Walton, associate medical director of precision genomics at Intermountain Health Care in Salt Lake City, also decried the technology offered by the two largest EHR vendors.

“We really need a home for genomic data in the EHR,” Walton said. “It takes a lot of work to get the [test] results in the right place … so they can actually be used.”

Intermountain uses Cerner. Pediatrician Walton previously was a clinical genetics specialist at Geisinger Health System in Pennsylvania, an Epic customer.

Without naming vendors during his AMIA presentation, Walton said that it can be quite difficult to get genomic data from the molecular laboratory to the EHR, though he cited lack of standards than more than anything that any vendor is doing.

A key problem, according to Walton, is that there is no standardization of genetic phenotypes. This makes it difficult to maintain variant classification across patients and reports, resulting in patients with the same variants receiving different care.

At both Geisinger and Intermountain, Walton ran pilots involving clinical decision support based, in part, on patient-specific genomic data. In both cases, he had to build custom interfaces from the EHR to laboratory information systems.

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

The standardization problem has also led to vendors taking different approaches to the same problem. According to Walton, Epic focuses more on population health, while Cerner has tried to build around the needs of clinical geneticists. “It would be nice if they could meet in the middle,” he said. In neither case have the needs of frontline physicians been adequately met.

For their part, the vendors did acknowledge some of their shortcomings, but said that they are making progress.

Robke said that he “would not argue” with Topol or Walton regarding whether legacy EHR vendors are innovative in genetics and genomics.

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

Epic, headquartered in Verona, Wisconsin, has created a genomics module, though it has not been universally adopted by its users.

Phil Lindemann, VP of business intelligence and analytics at Epic, worked on the Epic Beaker LIS for a decade. In Lindemann’s early days with the company, the Beaker team “spent a significant amount of time understanding the process to produce genetic results and essentially the wet-lab workflow that had to go into that,” he said.

As genomics has advanced, so has Epic’s inclusion of it, moving from single-variant results in the LIS to multivariant reports to cytogenetics and molecular diagnostics, and then, in 2018, to the genomics module in the core EHR. Lindemann said that about 90 percent of Epic clients are using versions of the EHR software that are less than a year old. The vendor updates its software every quarter or so.

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

Epic also has a dedicated genomics cloud to hold sequences and other large genomic datasets. “The idea is that that data can be used for research to make new discoveries and also to be reinterrogated and surfaced as knowledge evolves,” Procknow said. “Clinically actionable” data can be delivered to the EHR rather than the genomics cloud.

Institutions including the University of Pennsylvania, Mayo Clinic, and Arkansas Children’s Hospital have published papers about their use of Epic to bring structured genetic testing results to clinician workflows for pharmacogenomics and other forms of precision medicine.

Walton, who chairs AMIA’s Genomics and Translational Bioinformatics Working Group, did say that the vendors are making some progress on the genomics front, but added that a lack of certain standards remains a formidable barrier.

The standards issue actually presents an excellent opening for vendors to innovate, according to Cerner’s Robke. “I think there’s opportunity for us to get it right out of the chute versus trying to retrofit as things go forward,” he said.

Cerner chose the Health Level Seven International Fast Healthcare Interoperability Resources (FHIR) standard for transmitting data. Robke said that this decision puts Cerner “behind in the industry a little bit” because FHIR is not widely used among genomic labs. “Rightly or wrongly, we’re trying to push the industry that way,” he said.

Robke said that Cerner will be able to scale up quickly if FHIR does catch on.

Procknow said that Epic is being proactive with standards bodies. Epic is not a corporate member of GA4GH, but Epic VP of Genomics and Interoperability Peter DeVault is personally involved. Epic is also represented in the HL7 Genomics Workgroup.

“When there are places where the standards fall short or don’t communicate the right data, we’re working with our customers and with the labs to make additions and update the standards” via the standards organizations’ workgroups, Procknow said.

For example, customers have come to Epic looking for a place in the EHR to report mosaicism in genetic test results. “We’ve created a field for that and now we’re bringing it back to the [standards body’s] workgroup,” Procknow said.

Some of the consternation might come from the fact that standards updates take time and that it also can be slow to change organizational cultures and workflows as medicine advances.

Walton said that he has not heard from either vendor since his AMIA presentation in early November.

Cerner is in the process of being sold to Oracle for $28.3 billion. The publicly traded company, whose founding CEO Neal Patterson died in 2017, has had significant leadership turnover in recent years.  David Feinberg, whom Walton worked for at Geisinger, became CEO of Cerner in October. However, Walton said that he does not currently have a genomics-related contact with the firm, and a beta test of new Cerner technology that was supposed to have begun last summer remains in limbo.

This story first appeared in our sister publication, Genomeweb.