Data Element

Variant Type
Description

The data representing the type of genetic variation. Some examples of variant types include DNA, protein, chromosome.

Comment

This data element has…

This data element has support from the HL7® FHIR® CodeX™ Accelerator community. CodeX supported FHIR data standards for cancer, genomics and cardiovascular health have a rapidly growing footprint of traction and adoption. The CodeX community is rapidly growing its membership, with invested Member leaders driving implementation-focused use case pilots forward.

The Genomics data elements currently at Level 1 in USCDI (Gene Studied, Variant Data, Variant Type, Variant Interpretation) have representation in the following CodeX supported FHIR Implementation Guides (IGs):

The Genomics data elements currently at Level 1 in USCDI (Gene Studied, Variant Data, Variant Type, Variant Interpretation) are important to the genomics branch (GenomeX) of the CodeX Accelerator, currently with 2 active use case pilots:

  • Genomics Data Exchange Use Case:
    • https://confluence.hl7.org/display/COD/GenomeX+-+Genomics+Data+Exchange
    • Aims to develop scenario-based profiles/import specifications with the FHIR Genomics Reporting IG to share structured genomic data from a lab to receiving organizations (EHR/genomic data repository) so providers can use the data in patient care. Currently kicking off the initial minimum viable pilot which will include developing a standard data set across participants.
    • Current key aims for Phase 0 of this use case include testing sharing of synthetic genomics lab report with others (including EHRs) via FHIR. Goal to participate in 2024 January HL7 Connectathon
  • Genomics Operations Use Case
    • https://confluence.hl7.org/display/COD/GenomeX+-+Genomics+Operations
    • Aims to create an approach to utilize genomic data such that the FHIR Genomics Reporting IG operations will present a uniform interface and give providers easier access to actionable genetic variation information that could impact treatment options for patients. Currently building community and identifying specific problems and solutions.
    • Current key aims for Phase 0 of this use case include exchange of synthetic data demonstrate genomics operations capability for extracting genomics data from repositories for Molecular Tumor Board applications. Goal to participate in the 2024 January HL7 Connectathon.

 

Further pertinent links illustrating real world adoption and traction of the mCODE and Genomics Reporting IGs include:

Further mCODE traction/adoption & FHIR-based genomics data exchange in Germany (slide 12): https://confluence.hl7.org/display/COD/USCDI%3A+Comments+from+CodeX+Community?preview=/184913335/184927637/2023_09%20CodeX%20Overview%20for%20USCDIv5.pdf

rename?

Variant Type – consider renaming to Molecule type. Typically, the type of molecule that has been sequenced (amino-acid, RNA, DNA, polysaccharide, etc…) appears within reports. It is a very useful atomic data element. Sometimes, the phrase variant type is used to mean the structural type of the change. The current element name could be confusing.

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