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As Clinical Genomics Advances, HL7 Offers New FHIR Use Cases


CHICAGO (GenomeWeb) – Recognizing that clinical genomics is becoming more mainstream, standards development organization Health Level Seven International (HL7) has issued a series of use cases more suited for community hospitals and primary care clinics than previous, research-focused guidance.

The document comes on the heels of a new release of the Fast Healthcare Interoperability Resources (FHIR) standard, a specification that is playing an increasingly central role in the elusive journey toward a nationwide system of interoperable electronic health records.

FHIR Release 4 is more of a technical change to the previous version, as the standard has now passed a "normative ballot" for the purposes of American National Standards Institute recognition. That means that future changes to FHIR should be backward-compatible, according to Ann Arbor, Michigan-based HL7.

The previous version of FHIR, Release 3.2, was the first to include FHIR Genomics, a module to support interchange of machine-readable omics data. "It's really a unified clinical and genomic data standard," Gil Alterovitz, director of the Biomedical Cybernetics Laboratory at Harvard Medical School and co-chair of the HL7 Clinical Genomics Work Group, told GenomeWeb last year.

FHIR Genomics actually has been in the works for about five years, according to Alterovitz. For most of that time, HL7's genomics work has focused on sequencing data. Notably, the organization in 2017 published a document called the Domain Analysis Model: Clinical Sequencing to help IT developers understand when patients might be candidates for genomic sequencing.

The original set of use cases that HL7 described in 2017 included cancer profiling, specimen identification, family history, drug dosage calculators, sequencing for cytogenic marker identification, public health reporting, pharmacogenomics, and human leukocyte antigen typing. HL7 also recommended various nomenclature, reference databases, and vocabulary constraints for these uses.

Last month, HL7 formally announced Domain Analysis Model: Clinical Genomics, though the document actually was finalized in July 2018. "We used that [interim period] to help in building some of the FHIR things" into the model, Alterovitz said in a new interview.

The workgroup that Alterovitz chairs is tasked with identifying common use cases and workflows that could be improved with interoperable data standards like the ones HL7 develops. The core HL7 standard has always been a clinical communication specification, though use cases have evolved to include things of interest to chief information officers, chief medical officers, and chief medical informatics officers, not just IT specialists.

The new Domain Analysis Model: Clinical Genomics includes scenarios for preimplantation genetic diagnosis, whole-exome sequencing, RNA sequencing, and proteomics. It walks healthcare leaders through each step of each use case, describing how the data will affect clinicians, geneticists, laboratory professionals, and patients as health systems establish precision medicine programs.

"We found [commonalities] between all the different workflows that people must try to understand … if they're looking to get into precision medicine," Alterovitz said. "I think a bigger focus now is on point-of-care precision medicine."

The point of the new document is that clinical genomics is no longer the exclusive domain of oncologists and rare-disease specialists at teaching hospitals. "Now it might be a community hospital that wants to set up precision medicine," or a Kaiser Permanente type of integrated health system, Alterovitz said.

"They're not doing it for the research part. They're doing it for the care," he explained. "In the past, almost all genomic sequencing was done for research, but in the future it's going to be almost all for medical, just like it was for imaging in the past."

All of the use cases are intended to work with FHIR Genomics. In fact, according to Alterovitz, the 2017 sequencing model informed FHIR development.

"FHIR Genomics, the genomics part of FHIR, evolved from the [Domain Analysis Module] to support those cases," he said. "When you develop a specification, it's best to have use cases that you develop it to support."

Concurrently, the HL7 Clinical Genomics Work Group has been drafting an implementation guide for FHIR release 4. Alterovitz said that the standards organization recently sent that guide out to its members for balloting, and expects to finalize the guide later in 2019.

HL7 also indicated that it is addressing "uncertainty in the specific storage location" for clinical genomics information as well as formats for structuring omics data for "access on demand" by labs and clinicians alike. "Best practices in handling such considerations are being formulated within HL7 and include international input from across the spectrum of stakeholders," the organization said in a blog post.