Clinical Genomics: Molecular Definition (Jira PSS-2305)

n 2019 the Clinical Genomics Working Group launched the Information Modeling subgroup to explore the representation of discrete clinical omics data in FHIR. The evolution of that work has led to the development of information models that express semantics of the clinical genomics domain, which have been subsequently translated into FHIR.

This project aims to develop a comprehensive set of FHIR resources and profiles, including example data and supporting content, as well as an implementation guide that documents how the FHIR artifacts can be used to represent omic data. The work will primarily focus on "definitional" data that is outside the context of a clinical observation, and it be based on FHIR R5 and later releases. The focus of the work is on representing the genomic data itself rather than the contexts in which the data could be used.

In particular, this project may include:

- Development of the Molecular Definition (MolDef) resource

- Development of profiles of MolDef resource for: Sequence and Allele (which might be combined), Haplotype, and Genotype

- Development of a MolDef IG, outlining how those resources could be used and extended to support additional data types.

The MolDef IG would define discrete data structures that could be used 1) as part of a clinical test result, 2) as part of a research study, and 3) to represent patient-agnostic information from a knowledge base. The IG would include examples that illustrate how those discrete data structures could be used in each of those use cases, but it would defer to other IGs to capture the context of those use cases. For example, while the MolDef IG would demonstrate how its discrete structures for genomic data could be used to support clinical reporting, its scope would not include any patient or clinical context, including the clinical order or report (which are currently supported by the existing Genomics Reporting IG (R4b)).

At some future time the Clinical Genomics Working Group may decide to include the discrete data structures defined by the MolDef IG within the existing Genomics Reporting IG, by addition to and/or substitution of corresponding structures (e.g., Haplotype profile), which is anticipated to improve the ability to exchange structured genomic data produced by clinical testing. That decision will be subject to open discussion and formal vote(s). Note significant value of the MolDef IG is in the loose coupling between the well-defined, discrete data structures and the context in which the data are used, so the MolDef IG will add value to genomic data interoperability regardless of the decision(s) or timeline(s) related to its inclusion within the Genomics Reporting IG.