SMART on FHIR Genomics and the HL7 Clinical Genomics Work Group

• Work Group Home
• The FHIR guidance for genomics data (https://www.hl7.org/fhir/genomics.html) is a product of this work group.
• A description of the SMART on FHIR Genomics prototype is provided in Alterovitz (2015)¹. This highly cited reference is a good starting point to identify subsequent publications on similar topics.

ONC "Sync for genes"

In 2016 ONC launched Sync for Genes. A report describing the results of the first phase titled Sync for Genes: enabling clinical genomics for precision medicine via HL7® fast healthcare interoperability resources was released in 2017. This document outlines proposed plans for a national standard for exchanging genomic data in response to recommendations from the Precision Medicine Task Force.

Sync for Genes addresses a selection of the proposed items raised by the Task Force. Sync for Genes supports the ONC, NIH, and the Food and Drug Administration (FDA) toward fulfilling the Task Force’s recommendation to “[i]dentify opportunities for ONC to support our federal partners’ PMI efforts and related health IT/interoperability challenges, including National Cancer Institute, Food and Drug Administration, National Institutes of Health, and Department of Veterans Affairs.” Sync for Genes seeks to fulfill another recommendation — to “[i]dentify opportunities for ONC to collaborate with industry and pilot the use of standards to enable data donation and patient access through application programming interfaces (APIs) using standards such as FHIR and OAuth 2.0” — by utilizing FHIR Genomics and its leveraging of the SMART on FHIR Genomics framework as well as using the underlying security/privacy framework common to SMART on FHIR.

Notable features of the 2017 report include:

• Emphasis on an interoperability standard based on FHIR.
• Introduction of the concept of a Genomic Archive and Computer/Communication System (GACS): "A GACS acts in the same manner as a PACS — to store big data that is not suitable to store directly in an EHR."
• Presentation of a "list of the seven developed guidelines on standard development for enabling clinical genomics at point of care and facilitating precision medicine."
• Description of several Sync for Genes pilot projects using FHIR Genomics.

As of the end of 2021, ONC has published reports for a total of three phases of Sync for Genes (phase four launched in 2020). Phase 3, published in January 2021, was of particular interest, with a focus on sharing standardized genomic data generated by laboratories. This Phase included two pilot projects, one at Baylor College of Medicine, the other at the National Marrow Donor Program (NMDP):

The BCM-HGSC demonstration project created the eMERGE FHIR Specification, which established a standardized way to represent clinical genetic test results for sharing across networks. The NMDP demonstration project developed the HLA Reporting IG and a translator tool to convert HLA report data into FHIR format. The NMDP project efforts enable better representation of HLA data in FHIR and the exchange of this data in a standardized format.

The Phase 3 report identifies a number of challenges and areas requiring further development of the FHIR standard. Notably:

... detailed data elements such as precise definitions of genetic variants, the genomic regions covered by a given assay, the expression of novel results unique to a patient, and the actual genomic sequence were difficult to represent. As the demonstration projects exhibited, to support these data types, the FHIR specification needs to be further enhanced.

This report contains many useful references and a glossary of terms.

Miscellany

• Dolin et al (2021)² describes a utility for converting variant data in VCF format into FHIR.
• Swaminathan R, et al.³ compares the capabilities of the SMART Genomics API, Google Genomics, and the 23andMe API.
• The Association for Molecuar Pathology (AMP) released a statement titled AMP Position Statement on Variant Data Sharing in July 2021 that explores challenges and barriers to sharing and representing genetic variants.