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Genomic Data Standards Work Inches Forward With New HL7 GenomeX Initiative


CHICAGO – As precision medicine advocates struggle with what they see as a shortfall in standards to integrate genomic data into patient care, standards body Health Level Seven International (HL7) recently launched a program to facilitate interchange of machine-readable omics data following the Fast Healthcare Interoperability Resources (FHIR) specification.

The initiative, called GenomeX, will run pilots that focus on the collection and sharing of discrete, structured genomics data under the FHIR Genomics add-on to the core standard. GenomeX is housed within an HL7 FHIR accelerator called CodeX, a community of individuals and organizations with an interest in interoperability of all kinds of health data.

Stakeholders in this group will include molecular laboratories, care providers, payors, technology vendors, and patients, according to May Terry, principal for health informatics at Mitre, a McLean, Virginia-based nonprofit that operates federally funded R&D centers and is heavily involved with HL7.

"They're all going to differ in their level of detail of what they need to send or receive," Terry said. "I think the democratization of genomics data can be obviously achieved through consensus and standardization."

Steve Bratt, a Mitre principal who recently stepped down as leader of the organization's Health Standards and Interoperability Group, said he has also gotten interest from pharma companies, though he would not name any. "They're all interested in this ecosystem having a lot less friction than it has today, and to do that, we need standards."

The first use case will be moving data from a lab to a repository, either a dedicated genomics repository or an EHR itself. It is likely to be the latter because not all data in genome sequences will be clinically relevant. "You don't want to mess up the clinicians’ work with things they don't really need right now," Bratt explained.

"We're thinking about a use case where we get the data in from a lab to a repository, and then some subset of that data might be genomic data, maybe biomarkers transmitted to the EHR," added Bratt, who also is program manager for the CodeX FHIR accelerator.

Electronic health records have been a sticking point on the journey toward precision medicine. Providers have blamed EHR vendors for not doing enough to make genomic data machine-readable in patient records, while vendors have blamed a lack of standards for the difficulty of bringing genotypes into patient records.

The pilot is starting with labs because that is where genomic data originates. "If we can't get the labs involved and they're not interested in providing FHIR-based data exchange, then it's going to be hard to make a case for going forward [with GenomeX]," Bratt said.

Bratt said there is plenty of interest in the project, but he wants to see firm commitments, which the HL7 Clinical Genomics Work Group has not asked for yet. The request to participate in a CodeX pilot will come after the group convenes a meeting in the near future with a collection of interested parties.

Bratt is a self-described "lifelong standards wonk" who focuses on building communities of users around standards. He also is a former chief technology officer and president of standards development for GS1 as well as a former CEO of the World Wide Web Consortium.

"You can't just build standards and throw them out there," he said. Vendors have to embrace and incorporate them into their products and clinicians actually have to use the technology.

Bratt said patients are important stakeholders as well, and some patient advocacy groups have been involved in CodeX, though not yet in GenomeX. He said that he is "quite interested in the issue of equity," namely by helping to close the gap in quality of sequencing as well as actionability of data for patients of color.

"What we're doing here isn't going to solve that problem, but having easier accessible, standardized data should be a piece of helping to solve the problem," Bratt said.

HL7 is modeling GenomeX after the Minimal Common Oncology Data Elements, or mCODE, a collaboration among the American Society of Clinical Oncology (ASCO), Mitre, and the Alliance for Clinical Trials Oncology Foundation. Those partners, along with Intermountain Healthcare, ASCO's CancerLinQ nonprofit subsidiary, and others, have been working to establish consistent ways of storing and accessing half a dozen core types of information — including information on up to 17 genomic features — in the hopes of making it easier to find eligible clinical trial participants, compare EHR data across patients, and more.

Terry explained that mCODE is a FHIR-based information model for minimally actionable and interoperable elements of oncology data. "The combination and its specification of both genomic and clinical oncology data in one common set helps to capture, I think, the relevance of the most essential genomic elements for shared provider-patient decision-making at the point of care," she said.

Like the provider community, the vendor community itself is diverse, from EHRs to laboratory information systems to data analysis platforms. "Rather than saying they have adopted all of mCODE, each of these use cases will adopt pieces of it," explained Terry, a former medical informatics lead at Flatiron Health.

In turn, mCODE is following the lead of the United States Core Data for Interoperability (USCDI), a standardized set of data elements for data interoperability that stems from the 21st Century Cures Act. Those regulations addressing information blocking took effect a year ago and will become mandatory for electronic health data exchange on Oct. 6, 2022. 

That law and the anti-information-blocking rule it spawned encouraged the use of application programming interfaces and standards such as FHIR to encourage the interoperability of health information to support coordinated care and, indirectly, the practice of precision medicine.

A draft update to USCDI includes what Terry called "initial, very basic elements that are genomics variant-related" that didn't make the current, second version of the dataset. "It would be the first step of many to help bring in [genomics] as part of the core set … especially as it relates to oncology," Terry said.

Mitre is involved in many HL7 projects, as well as government initiatives including the Biden administration's revived Cancer Moonshot.

Terry said that the Cancer Moonshot "definitely makes the Minimal Common Oncology Data Elements very relevant with some of the goals that [President Joe Biden] has," including reducing the incidence of cancer by 50 percent by 2050.

She called mCODE "kind of unique in its approach" because it specifies a minimal actionable set of genomic data. "We can have as part of the mCODE implementation guide that subset of that larger specification that goes to the HL7 Genomics reporting implementation guide and reference something that's a lot more complex," Terry said.

This is where community-building comes in. Bratt said that more than 40 health systems wrote to Epic Systems CEO Judith Faulkner to get that EHR vendor to support mCODE. "Epic is now shipping with increasing parts of mCODE to support very specific uses that their customers are interested in," he said. Several radiation therapy equipment manufacturers, including Varian Medical Systems, Elekta, and RaySearch Laboratories, are following customer requests to adopt mCODE.

"I think getting the labs involved is really critical," Bratt said. "We definitely need to get structured genomics data in the hands of clinicians and researchers much quicker and easier than we do today."

Bratt said it would be "in everyone's best interest, whether they're researchers from pharma or caregivers, to have that data available at their fingertips and actionable, bringing clinical decision support systems and pathways."