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A 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.
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GeneticObservation |
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Field Name |
Field Type |
Cardinality |
Description |
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AssessedCondition1 |
Resource (Condition) |
1 |
Condition described by this observation |
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SourceSeq2 |
Resource (Sequence) |
0..* |
Sequence resource linked to this observation |
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Interpretation3 |
CodeableConcept |
0..* |
Interpretation of the effect of this variant (SNOMED-CT) |
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Comment3 |
String |
0..* |
Comments on this variant |
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DNASequenceVariation4 |
String |
0..* |
HGVS nomenclature for cDNA variant. |
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GeneId4 |
CodeableConcept |
0..* |
HGNC identifier and symbol |
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VariantTranscriptReferenceSequenceId4 |
CodeableConcept |
0..* |
cDNA reference sequence identifier either RefSeq or ENSEMBL. |
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DNASequenceVariationType4 |
CodeableConcept |
0..* |
Classification of variant change using LOINC Answer List values 48019-4 or Sequence Ontology values. |
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DNARegionName4 |
String |
0..* |
Gene region containing the variant e.g. Exon 19. |
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ProteinReferenceSequenceId4 |
CodableConcept |
0..* |
Protein reference sequence identifier either RefSeq or ENSEMBL. |
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AminoAcidChange4 |
String |
0..* |
HGVS nomenclature for amino acid change. |
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AminoAcidChangeType4 |
CodableConcept |
0..* |
Classification of variant change using LOINC Answer List values 48019-4 or Sequence Ontology values. |
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VariationId4 |
CodableConcept |
0..* |
Variant identifier in ClinVar, dbSNP or COSMIC. |
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AlleleName4 |
String |
0..* |
Common name for variant for display purposes. |
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GenomicSourceClass4 |
CodableConcept |
0..* |
The genomic class of the variant: Germline, Somatic, or Prenatal. Associated with LOINC answer list: 48002-0. |
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AllelicState4 |
CodableConcept |
0..* |
Level of occurrence of the DNA variation in relation to the genomic context. LOINC answer list: LOINC 53034-5 |
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Subject3 |
Resource (Patient) |
1 |
Genetic lab’s patient ID for this sequence |
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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.
Gets a GeneticObservation
HTTP Request: GET /Procedure/{Id}
Parameters:
Id - ID of SequenceLab to get
Permission Scope: user/Observation.read or patient/Observation.read
Request Body: None
Response Body: If successful, returns the requested GeneticObservation resouce
Creates a GeneticObservation
HTTP Request: POST /Observation
Parameters: None
Permission Scope: user/Observation.create or patient/Observation.create
Request Body: Supply a GeneticObservation Resource
Response Body: None
Updates a GeneticObservation
HTTP Request: PUT /Procedure/{Id}
Parameters:
Id - ID of GeneticObservation to update
Permission Scope: user/Observation.write or patient/Observation.write
Request Body: GeneticObservation resource with updated values
Response Body: None
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 Scope: user/Observation.read or patient/Observation.read
Request Body: None
Response: If successful, returns the GeneticObservations that match the search parameters