GeneticObservation


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    Resource Representation
    Methods
        Get
        Create
        Update
        Search

Resource Representation

GeneticObservation resource contains information that associates the patient's observed phenotype to the genotype. A Genetic Observation can be for either a Somatic or Germline mutation. If Somatic, variantGene must be defined. If Germine, variantSequence must be defined. GeneticObservation is an extension of the Observation resource.

GeneticObservation

Field Name

Field Type

Cardinality

Description

AssessedCondition1

Resource (Condition)

1

Condition described by this observation

SourceSeq2

Resource (Sequence)

0..*

Sequence resource linked to this observation

Interpretation3

CodeableConcept

0..*

Interpretation of the effect of this variant (SNOMED-CT)

Comment3

String

0..*

Comments on this variant

DNASequenceVariation4

String

0..*

HGVS nomenclature for cDNA variant.

GeneId4

CodeableConcept

0..*

HGNC identifier and symbol

VariantTranscriptReferenceSequenceId4

CodeableConcept

0..*

cDNA reference sequence identifier either RefSeq or ENSEMBL.

DNASequenceVariationType4

CodeableConcept

0..*

Classification of variant change using LOINC Answer List values 48019-4 or Sequence Ontology values.

DNARegionName4

String

0..*

Gene region containing the variant e.g. Exon 19.

ProteinReferenceSequenceId4

CodableConcept

0..*

Protein reference sequence identifier either  RefSeq or ENSEMBL.

AminoAcidChange4

String

0..*

HGVS nomenclature for amino acid change.

AminoAcidChangeType4

CodableConcept

0..*

Classification of variant change using LOINC Answer List values 48019-4 or Sequence Ontology values.

VariationId4

CodableConcept

0..*

Variant identifier in ClinVar, dbSNP or COSMIC.

AlleleName4

String

0..*

Common name for variant for display purposes.

GenomicSourceClass4

CodableConcept

0..*

The genomic class of the variant: Germline, Somatic, or Prenatal. Associated with LOINC answer list: 48002-0.

AllelicState4

CodableConcept

0..*

Level of occurrence of the DNA variation in relation to the genomic context. LOINC answer list: LOINC 53034-5

Subject3

Resource (Patient)

1

Genetic lab’s patient ID for this sequence

Specimen3

Resource (Specimen)

1

Specimen source of data

 

1 Adopted from SMART into the HL7 Clinical Genomics Standard Profile for Genetics. Where elements were constrained for integration into the observation profile which is limited to genetic information, the FHIR DSTU2 name is in parenthesis.

2 Sequence and Sequencing Lab Resources are undergoing HL7 review for inclusion in FHIR DSTU3.

3 These components are inherited from the FHIR Observation resource.

4 These components focus on HL7 standard reporting findings based on traditional genetic testing technologies.

Methods

Get

Gets a GeneticObservation

HTTP Request:    GET /Procedure/{Id}

Parameters: 
  Id - ID of SequenceLab to get

Permission Scopeuser/Observation.read or patient/Observation.read

Request Body: None

Response Body: If successful, returns the requested GeneticObservation resouce

Create

Creates a GeneticObservation

HTTP Request:    POST /Observation

Parameters: None

Permission Scopeuser/Observation.create or patient/Observation.create

Request Body: Supply a GeneticObservation Resource

Response Body: None

Update

Updates a GeneticObservation

HTTP Request:    PUT /Procedure/{Id}

Parameters: 
  Id - ID of GeneticObservation to update

Permission Scopeuser/Observation.write or patient/Observation.write

Request Body: GeneticObservation resource with updated values

Response Body: None

Search

Searches for a GeneticObservation

HTTP Request:    GET /Observation

Parameters: 
 
AssessedCondition - Condition assessed
  Date - Date of this observation
  Name - Name of the observation
  Performer - Person who performed the observation
  Related - Observations related to this observation
  Reliability - Reliability of the observation
  Specimen - Specimen used for the observation
  Status - Status of the observation
  Subject - Subject the observation is on
  Value - Value of the observation

Permission Scopeuser/Observation.read or patient/Observation.read

Request Body: None

Response: If successful, returns the GeneticObservations that match the search parameters