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Owning work group name:
Clinical Genomics
Committee Approval Date:
Tuesday, July 12th 2022
Contributing or Reviewing Work Groups:
Orders and Observations
FHIR Resource Development Project Insight ID:
1217
Scope of coverage:
The scope of this resource covers human genomic metadata that could be applicable to any delivery environment or locale where genomic analyses are performed.
This resource captures important information on performed genomic tests at a higher level of detail than could be done by Procedure. It allows tracking what types of sequencing were performed on which specimen and which genomic regions, and it can provide downstream systems with references to sequencing files that were generated throughout the study. A genomic study might comprise one or more analyses, which may vary in method (e.g., karyotyping, CNV, or SNV detection), performer, software or sequencing devices used, regions targeted.
A genomic study might be based on one or more serviceRequests or care plans. The reasons for performing a genomic study might be driven by specific Conditions or Observations. Although the subject of the genomics study is the focus of the study, other Patients and/or Specimen may be listed in analyses as required, for example in a trio test, de novo mutation detection, or tumor-normal testing.
The regionStudied and regionCalled elements can refer to DocumentReference instances carrying BED files. Other types of files used in an analysis can be provided similarly, and listed either as inputs or outputs.
Detailed information about the results of the analyses may be represented by Observations and gathered in a DiagnosticReport. Both resources may refer back to the originating GenomicStudy to allow navigation.
RIM scope:
out of scope for the RIM
Resource appropriateness:
We find this resource to be appropriate as a necessary adaptation to genomics of the workflow enabled by the ImagingStudy resource.
Expected implementations:
This resource is expected to be implemented by any systems that have a business need to track and expose genomic sequencing files or metadata and support FHIR R5.
Content sources:
This resource collects metadata and references to genomic files and formats standardized by the Global Alliance for Genomics and Health (GA4GH).
Example Scenarios:
- Ability to provide details about an item in a test catalog
- Ability to provide details about a performed test
- Ability to say that a genomic finding came from a particular kind of test
- Ability to say that a genomic finding came from a particular test instance (and that many findings came from the same test instance)
- Ability to tell when absence of evidence of genomic variants equals evidence of absence
A real world example scenario:
- In March 2019, a patient is found to have a lung mass on CXR, and undergoes lung biopsy. WES of a 300 gene panel is performed on the biopsy specimen, and analyzed for simple variants (SNV, MNV, InDel). For technical reasons, the gene PIK3CB was deemed uncallable.
- In July 2020, the same patient presents with a headache, and a mass is found on head CT. Biopsy is consistent with metastatic lung cancer. WES of a 420 gene panel is performed on the biopsy specimen, and analyzed for simple variants (SNV, MNV, InDel) and for Copy Number Variants. For technical reasons, PIK3CB, APC, MEN1, and portions of EGFR were deemed uncallable.
- To be eligible for a particular clinical trial, patients must have an EGFR exon 19 (NC_000007.14:55174721-55174820) deletion. The patient's oncologist finds no simple or structural variants in the region of EGFR exon 19, and asks staff bioinformaticist to confirm whether EGFR, including exon 19, was studied as part of the July 2020 test. (Results indicate that EGFR was studied, but exon 19 was deemed uncallable).
Resource Relationships:
A main function of GenomicStudy is to provide important metadata for one or more genomic analysis pipelines. It can include DocumentReference instances that carry as Attachments various genomic files used in clinical genomic pipelines and can encode and surface high-level settings and methodology information. Device is used to represent both hardware and software used in the sequencing and in the analyses.
It is intended that this resource be referenced by Observation and DiagnosticReport similarly to how ImagingStudy is currently referenced on those resources. Of note, the results of the study would be captured in Observations and referenced on a DiagnosticReport.
Important contextual references include Patient, Specimen, Encounter, ServiceRequest, Practitioner, and Organization.
Observation or Condition may also be referenced from genomic study to designate a given reason for performing the study.
We also intend to support the event-definition workflow pattern by referencing PlanDefinition(s) via the ‘instantiatesCanonical’ relationship when implementers wish to describe more specifics of the pipelines and devices used in the analysis.
Resource Boundaries:
Procedure may be used in a limited manner for a subset of use cases.
Timelines:
Workgroup had determined complete for approval (at Maturity 0) for R5 ballot.
gForge Users:
When Resource Proposal Is Complete:
When you have completed your proposal, please send an email to FMGcontact@HL7.org