This page is part of the Genetic Reporting Implementation Guide (v0.3.0: STU 1 Ballot 2) based on FHIR R4. The current version which supercedes this version is 2.0.0. For a full list of available versions, see the Directory of published versions

Artifact List

Artifact Packages

This page provides a list of the FHIR artifacts defined as part of this implementation guide.

General Profiles

General constraints on FHIR resources to be adhered to as part of the CG implementation guide that apply regardless of what area(s) of genomics are of interest

  •  Genetic Observation Common Properties Base profile that defines characteristics shared by all genetic observations
  •  Genomics Report Defines the overall genomic report
  •  Specimen Constraints on Specimen for use with clinical genomics reporting
  •  Recomended Followup Task describing the followup that is recommended
  •  Request for Genetics Test The lab order or request that triggered the execution of the genetics test
  •  Genomics Panel Organizes information within a genetic report
  •  Genomic analysis overall interpretation Provides a coarse overall interpretation of the genetic results reported.
  •  Deletion-duplication overall interpretation Provides an overall interpretation of whether any deletions or duplications were found as part of the genetic analysis
  •  Computable Genetic Finding Properties common to genetic findings whose results are expressed as computable discrete elements (e.g. genotypes, haplotypes, variants, etc.)
  •  Haplotype Assertion of a particular haplotype on the basis of one or more variants
  •  Genotype Assertion of a particular genotype on the basis of one or more variants or haplotypes
  •  Cytogenetic Nomenclature Fully describes a variant with a single code. Typically a large variant such as a mosaic, abnormal chromosome numbers, etc.
  •  Complex Variant A variant consisting of multiple independent consecutive variations
  •  Described Variant Details about a set of changes in the tested sample compared to a reference sequence.
  •  Sequence Phase Relationship Indicates whether two entities are in Cis (same strand) or Trans (opposite strand) relationship to each other
  •  Genetic Impact Abstract profile for observations describing the impact of one or more genetic observations.
  •  Inherited Disease Pathogenicity Provides an indication of whether there's a pathologic risk associated with a particular genotype, haplotype, variant or combination there-of, and if so, what the associated pathology is.
  •  Region Studied Provides a description of the region studied.

Somatics

Profiles related to the reporting of somatic genetic issues

  •  Somatic Impact Finding of whether a particular somatic genotype/haplotype/variation or combination-thereof provides evidence for or against a particular type of cancer or the effectiveness of different interventions
  •  Somatic Diagnostic Impact Finding of whether a particular somatic genotype/haplotype/variation or combination-thereof supports or opposes the diagnosis of a particular cancer
  •  Somatic Prognostic Impact Finding of whether a particular somatic genotype/haplotype/variation or combination-thereof predicts a particular outcome for the specified cancer - either on its own or in conjunction with one or more interventions
  •  Somatic Predictive Impact Finding of whether a particular somatic genotype/haplotype/variation or combination-thereof predicts the impact of a specified medication or combination of medications

Pharmacogenomics

Profiles for reports relating to genetic impact on medication use and effectiveness

  •  Medication Impact Abstract profile with common properties for observations that convey the potential impact of a genetic characteristics on a medication
  •  Medication Metabolism Impact Assertion of the expected impact of a particular genotype on the ability of the subject to metabolize medications
  •  Medication Transporter Impact Assertion of the expected impact of a particular genotype on the ability of the subject to actively transport medications
  •  Medication Efficacy Impact Assertion of the expected impact of a particular genotype on the efficacy of medications for the subject
  •  High Risk Allele Assertion of whether the patient has a high-risk allele
  •  Medication Usage Implication Task describing what sort of change (if any) should be made in a patient's medication based on an identified genotype
  •  Current Medication MedicationStatement describing a med potentially being taken by the patient that may require adjustment

Cytogenomics

Profiles for reporting cytogenetic results

  •  Copy Number Change Details about the copy number pair, such as the base pair start and end coordinates of where the change occurred.
  •  Device Microarray Platform Information about a micro-array platform used as part of copy number change testing
  •  Device FISH Probe Information about the probe used in a FISH test

Extensions

Extensions defined as part of the CG implementation guide

  •  Related Artifact Captures citations, evidence and other supporting documentation for the observation or report
  •  Recommended Action - DiagnosticReport References a proposed action that is recommended based on the results of the diagnostic report
  •  Supporting Information Additional information relevant to interpreting/understanding the report
  •  Focus Allows an observation to be made about multiple things.
  •  Recommended Action - Observation References a proposed action that is recommended based on the results of the observation.

Example(s)

Example(s) showing the use of the CG profiles

  •  Example - Genomics Reporting Test instance showing data from the CG v2 spec
  •  Example - Pharmacogenomics Pharmacogenomic Report Example instances
  •  Example - Full Bundle HLA genotyping for HLA-A, HLA-B, and HLA-C, using GLStrings Full Bundle HLA Typing Example
  •  Example - HLA genotyping for HLA-A, HLA-B, and HLA-C, using GLStrings DiagnosticReport HLA Typing Example
  •  Example - HLA genotyping for HLA-A, using GLStrings HLA-A genoyping Example: HLA-A*03:01:01:01+HLA-A*30:01:01
  •  Example - Observation for a single HLA-A allele HLA-A allele observaation: HLA-A*03:01:01:01
  •  Example - Buccal swab for HLA typing Specimen example: Buccal swab for HLA typing
  •  Example - Service request for high-resolution HLA-A genotyping ServiceRequest example: High-resolution HLA-A genotyping