ObservationGenetics FHIR Profile Proposal

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ObservationGenetics

The ObservationGenetics profile extends the Observation resource to enable reporting of structured genetic test results. In addition, the genetics profile contextualizes well established standards from the field of clinical genetics into the standards of healthcare (e.g. HGNC - HUGO Gene Nomenclature Committee's international standard for gene names, symbols, and identifiers).

Genetic Standards and Resources include:

  • Variant Databases: dbSNP , ClinVar , and COSMIC
  • Reference Sequences: RefSeq and ENSEMBL
  • Gene Symbols and Identifiers: HGNC - Human Genee Nomenclature Committee
  • Variant Nomenclature: HGVS nomenclature from the Human Genome Variantion Society
  • Locus: Gene

Profile balloting plans

STU3

Profile Details

The ObservationGenetics profile supports reporting of a DNA variant at the genomic, cDNA, and protein change level. In addition, a condition context may be provided, as AssessedCondition. For large genomic tests, a condition may be used as an input into the analytic pipeline to aid in the identification of clinically relevant variants related to the test order. It is strongly encouraged to provide all available information in this profile for any reported variants, because receiving systems (e.g. discovery research, outcomes analysis, and public health reporting) may use this information to normalize variants over time or across sources. However, these data should not be used to dynamically correct/change variant representations for clinical use outside of the laboratory, due to insufficient information.

Profiled Resource(s)

The following FHIR resource is profiled:

Constraints to be Applied

The following constraints are applied to the FHIR resources as necessary:

  • Constrain the cardinality of the data elements within the resource.
  • Constrain the mustSupport attribute of the data elements within the resource.
  • Define searchParameters as necessary for the resource.
  • Constrain vocabularies for the resources as applicable.

Extensions to be Applied

The following extensions are applied to the Observation resource as appropriate:

  • Clinical genomics specific extensions.

Example Scenarios

  • Query Examples for the Observation resource.
  • Query Result Examples for the Observation resource.

Scope of coverage

  • Subject: patient
  • Disciplines: Patient Care, Clinical Research, Public Health
  • Delivery Environment: Inpatient, Ambulatory, Community, Emergency, etc.

Realm

Clinical genomics.

Ownership

Owning committee name

Clinical Genomics

Contributing or Reviewing Work Groups

  • None

Expected implementations

gForge Users

  • Gil Alterovitz
  • Gaston Fiore

FHIR Profile Development Project Insight ID

  • 1110

Plans

Timelines

  • July 2016

Balloting Requirements

  • Ballot with next FHIR DSTU or Normative Edition

Desired Ballot Date

  • End 2016

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