Major electronic health record providers insist that they have successfully met the needs of the emerging field of clinical genomics despite obstacles, including uncertainty about who will pay for genomic testing, lack of data standardization, and the generally slow pace of change in healthcare.

Catherine Procknow, head of genomics products at Epic Systems, said: “We work closely with customers, genetic testing laboratories, and standards agencies…Go beyond the PDF result report to truly bring discrete genetic testing data to Epic.”

Bob Robke, vice president of Cerner’s clinical enterprise, said that the entire healthcare industry is still struggling to understand how to incorporate genomics into patient care. Robke pointed out that pharmacogenomics has not been accepted as he hoped, because vendors often have questions about who will pay for testing. “When we start to see this trend change, you will see that we are [pharmacogenomics],” He said.

Robke said that in recent years, some incremental improvements have been made to the core Cerner Millennium EHR products. For example, he said, the company based in North Kansas City, Missouri, has responded to customer requests to include somatic cell test results in the EHR for chart review.

At the American Medical Informatics Association (AMIA) annual symposium in November, Epic and Cerner became some acrimonious targets related to their processing of genomic data. To a certain extent, the supplier agreed with some criticisms, but said that more extensive industry cooperation is needed to provide better support for precision medicine.

In the opening keynote speech of the AMIA Conference in San Diego, Eric Topol, director and founder of the Scripps Research and Translational Institute, condemned the “informatics duopoly” even though he did not specifically name Epic and Cerner-This does not correctly provide all the data that clinicians need to practice more accurate medicine.

“There is too much homeless data out there,” said Topol, a cardiologist and expert on genomics and digital technology integration. In a subsequent email, he explained that the “homeless” data includes genomics, wearable sensor readings, environmental factors, and other items that are not suitable for traditional EHR platforms.

Topol said that the future he described in an article 2019 year Natural medicine Paper Until EHR has all these auxiliary data to provide to the artificial intelligence engine, it can realize “high-performance medicine”, in which the “digital health coach” will guide patients to better health. At AMIA, he expressed the hope that some new entrants including Graphite Health, Truveta and Tempus may break Epic-Cerner’s duopoly; Topol is a paid consultant for Tempus.

At another AMIA meeting, Nephi Walton, associate medical director of precision genomics at Intermountain Health Care in Salt Lake City, also condemned the technology provided by the two largest EHR vendors.

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

Intermountain uses Cerner. Pediatrician Walton was previously a clinical genetics specialist at Geisinger Health System in Pennsylvania and a client of Epic.

Walton did not specify a supplier in his AMIA presentation. He said that getting genomic data from molecular laboratories to EHR can be very difficult, although he believes the lack of standards is more important than what any supplier is doing.

Walton believes that a key issue is that genetic phenotypes are not standardized. This makes it difficult to maintain the classification of variants between patients and reports, resulting in patients with the same variant receiving different care.

At Geisinger and Intermountain, Walton conducted pilot trials involving clinical decision support, based in part on patient-specific genomic data. In both cases, he must build a custom interface from the EHR to the laboratory information system.

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

Standardization issues have also led suppliers to adopt different approaches to the same problem. According to Walton, Epic is more concerned with population health, while Cerner is trying to build around the needs of clinical geneticists. “It would be nice if they could meet in the middle,” he said. In both cases, the needs of first-line doctors have not been fully met.

As far as the suppliers are concerned, they did acknowledge some shortcomings, but said they are making progress.

Robke said he “will not argue” with Topol or Walton about whether traditional EHR vendors are innovative in genetics and genomics.

He suggested that Cerner might turn to industry partners for help in the field of clinical genomics, possibly through its Cerner Open Developer Experience (CODE) program.For CODE, the supplier has an app store for add-ons Including genomics applications, such as 2bPrecise. (Laboratory and software company AccessDx Bought 2bPrecise From Allscripts Healthcare Solutions, another major EHR provider, in August. )

Epic, based in Verona, Wisconsin, created a Genomics Module, Although it has not been widely adopted by users.

Phil Lindemann, Epic’s vice president of business intelligence and analytics, has worked on Epic Beaker LIS for ten years. In the early days of Lindemann in the company, the Beaker team “spent a lot of time to understand the process of generating genetic results and the wet laboratory workflow that must be entered,” he said.

With the advancement of genomics, Epic also included it, from univariate results in LIS to multivariate reports in cytogenetics and molecular diagnostics, and then in 2018, to the genomics module in the core EHR. Lindemann said that approximately 90% of Epic customers are using the EHR software version less than a year old. The supplier updates its software every quarter or so.

Lindemann said that Epic has worked with its customers and major molecular diagnostic laboratories including Tempus and Foundation Medicine to find out how to bring genomic information to Medical points. He added that these laboratories are “leading in how to interpret and understand genomic information for clinicians because they know that this knowledge gap must be bridged over time.”

Epic also has Dedicated Genomics Cloud Save sequences and other large genomic data sets. “The idea is that these data can be used for research to make new discoveries, and be re-inquired and surfaced as knowledge develops,” Prokno said. “Clinically actionable” data can be sent to the EHR instead of the genomics cloud.

Institutions include University of Pennsylvania, Mayo Clinic, and Arkansas Children’s Hospital A paper on their use of Epic to bring structured genetic testing results into the workflow of clinicians in pharmacogenomics and other forms of precision medicine has been published.

Walton is the chair of the AMIA Genomics and Translational Bioinformatics Working Group. He did say that vendors have made some progress in genomics, but added that the lack of certain standards is still a huge obstacle.

According to Robke of Cerner, standards issues actually provide an excellent opportunity for suppliers to innovate. He said: “I think we have the opportunity to take it out of the chute instead of transforming it as things progress.”

Cerner selected the Health Level 7 International Fast Medical Interoperability Resource (FHIR) standard to transmit data. Robke said that this decision made Cerner “a little bit behind in the industry” because FHIR is not widely used in genome laboratories. “Whether right or wrong, we are working hard to promote this industry,” he said.

Robke said that if FHIR really becomes popular, Cerner will be able to quickly scale up.

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Procknow stated that Epic is actively working with standards bodies. Epic is not a corporate member of GA4GH, but Peter DeVault, Epic’s vice president of genomics and interoperability, is personally involved. Epic is also represented in the HL7 Genomics Working Group.

“When there are insufficient standards or where the correct data cannot be communicated, we are working with customers and laboratories to add and update standards through the working groups of the standards organization,” Prokno said.

For example, a customer came to Epic to find a place in the EHR to report mosaicism in genetic test results. “We created a field for this, and now we bring it back [standards body’s] Working group,” Prokno said.

Some panic may come from the fact that it takes time for standards to be updated, and with the advancement of medicine, changes in organizational culture and work processes may also be slow.

Walton said that since his AMIA speech in early November, he has not heard from any supplier.

Cerner is being sold to Oracle for $28.3 billion. Neil Patterson, the founding CEO of this public company, passed away in 2017, and the leadership has undergone major changes in recent years. Walton’s David Feinberg, who works for Geisinger, became Cerner’s CEO in October. However, Walton said that he currently has no genomics-related connection with the company, and the Beta test of the new Cerner technology, which should have started last summer, is still in an uncertain state.

This story first appeared in our sister publication, Genome Network.