[Observation: templateId 2.16.840.1.113883.10.20.20.2]
The ClinicalGenomicStatement template serves the structured portion of the GTR Implementation Guide. At its core, there is a genetic observation finding (result), e.g., a genetic variation, which can be associated with an indication for performing this genetic observation, as well as be associated with the interpretation of the observation finding. In addtion, it is possible to associate a specimen and genomic source class with the core genetic finding as well as performers of the genetic observation.
Due to the complexity of the interpretation of genetic observations, this template disallows the use of the
interpretationCode attribute, rather uses an association to InterpretivePhenotype. Nevertheless, due to the specificity of the interpretation, sub-templates of this template further constrain it by using InterpretivePhenotype sub-templates. For example, ClinicalGenomicStatementGeneticVariation is a sub-template of ClinicalGenomicStatement and is associated with InterpretivePhenotypeGeneticVariation which is a sub-template of InterpretivePhenotype. All clinical genomic statement (CGS) structured data items shall be part of CGS instances so that parsing applications can find the full semantics explicitly represented in one coherent structure. Sub-sections such as Indications, Interpretations and Specimen are mainly for presenting narrative, but they may also contain structured data. In this way, it is possible to have less redundant documents, e.g., in the case where all tests reported in a GTR document have the same indication, an Indications section in the Summary section consists of a full-blown indication observation which all CGS indication observations reference.
CGS structured data may point to the respective narrative in sub-sections (by means of XML ID).
1. SHOULD contain zero or one [0..1] entryRelationship
a. Contains @typeCode="RSON" RSON
b. Contains exactly one [1..1] Indication Observation (templateId: 2.16.840.1.113883.10.20.20.3.3) 2. SHOULD contain zero or one [0..1] entryRelationship
a. Contains @typeCode="SPRT" SPRT
b. Contains exactly one [1..1] Interpretive Phenotype (templateId: 2.16.840.1.113883.10.20.20.2.5) 3. SHOULD contain zero or one [0..1] entryRelationship
a. Contains @typeCode="SUBJ" SUBJ
b. Contains exactly one [1..1] Genomic Source Class (templateId: 2.16.840.1.113883.10.20.20.3.2) 4. Contains exactly one [1..1] code
5. Contains zero or more [0..*] value
1. Contains exactly one [1..1] @classCode with data type ActClassObservation
2. Contains exactly one [1..1] @moodCode with data type x_ActMoodDocumentObservation 3. Contains exactly one [1..1] code
4. Contains zero or more [0..*] value
5. SHOULD contain zero or one [0..1] entryRelationship
a. Contains @typeCode="RSON" RSON
b. Contains exactly one [1..1] Indication Observation (templateId: 2.16.840.1.113883.10.20.20.3.3) 6. SHOULD contain zero or one [0..1] entryRelationship
a. Contains @typeCode="SPRT" SPRT
b. Contains exactly one [1..1] Interpretive Phenotype (templateId: 2.16.840.1.113883.10.20.20.2.5) 7. SHOULD contain zero or one [0..1] entryRelationship
b. Contains exactly one [1..1] Genomic Source Class (templateId: 2.16.840.1.113883.10.20.20.3.2)
<?xml version="1.0" encoding="UTF-8"?>
<observation xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="urn:hl7-org:v3" xsi:schemaLocation="urn:hl7-org:v3 CDA.xsd" classCode="OBS" moodCode="EVN">
<templateId root="2.16.840.1.113883.10.20.20.2.1"/> <id root="2.16.840.1.113883.18.12.7.30.9.8.1"/>
<code code="55208-3" codeSystemName="LOINC" displayName="DNA Analysis Discrete Sequence Variant Panel"/>
<statusCode code="completed"/>
<effectiveTime value="200512011500"/> <entryRelationship typeCode="SUBJ">
<observation classCode="OBS" moodCode="EVN">
<code code="48018-6" codeSystemName="LOINC" displayName="Gene Identifier"/>
<value xsi:type="CD" code="GJB2" codeSystemName="HUGO"/> </observation>
</entryRelationship>
<entryRelationship typeCode="SUBJ">
<observation classCode="OBS" moodCode="EVN">
<code code="51958-7" codeSystemName="LOINC" displayName="Transcript Reference Sequence Identifier"/>
<value xsi:type="CD" code="NM_004004.5" codeSystem="REFSEQ" codeSystemName="NCBI Reference Sequence"/>
</observation> </entryRelationship>
<entryRelationship typeCode="SUBJ">
<observation classCode="OBS" moodCode="EVN">
<code code="48003-8" codeSystemName="LOINC" displayName="DNA Sequence Variation Identifier"/>
<value xsi:type="CD" code="rs72474224" codeSystemName="dbSNP"/> </observation>
</entryRelationship>
<entryRelationship typeCode="SUBJ">
<observation classCode="OBS" moodCode="EVN">
<code code="48004-6" codeSystemName="LOINC" displayName="DNA Sequence Variation"/>
<value xsi:type="CD" code="109G>A" codeSystemName="HGVS nomenclature for the description of sequence variations"/>
</observation> </entryRelationship>
<entryRelationship typeCode="SUBJ">
<observation classCode="OBS" moodCode="EVN">
<code code="48019-4" codeSystemName="LOINC" displayName="DNA Sequence Variation Type"/>
<value xsi:type="CD" code="LA6690-7" codeSystemName="LOINC" displayName="Substitution"/>
</observation> </entryRelationship>
<entryRelationship typeCode="SUBJ">
<observation classCode="OBS" moodCode="EVN">
<templateId root="2.16.840.1.113883.10.20.20.2.1.1"/>
<code code="48005-3" codeSystemName="LOINC" displayName="Amino Acid Change"/>
<value xsi:type="CD" code="Val37Ile"/> </observation>
</entryRelationship>
<entryRelationship typeCode="SUBJ">
<observation classCode="OBS" moodCode="EVN">
<code code="48006-1" codeSystemName="LOINC" displayName="Amino acid change type"/>
</observation> </entryRelationship>
<entryRelationship typeCode="SUBJ">
<observation classCode="OBS" moodCode="EVN">
<code code="47999-8" codeSystemName="LOINC" displayName="DNA Region Name"/>
<value xsi:type="ST">Exon 2</value> </observation>
</entryRelationship>
<entryRelationship typeCode="SUBJ">
<observation classCode="OBS" moodCode="EVN">
<code code="53034-5" codeSystemName="LOINC" displayName=" Allelic State"/>
<value xsi:type="CD" code="LA6705-3" codeSystemName="LOINC" displayName="Homozygous"/>
</observation> </entryRelationship>
<entryRelationship typeCode="RSON">
<observation classCode="OBS" moodCode="EVN"> <id root="2.16.840.1.113883.18.12.7.30.9.2.1"/> <code/>
</observation> </entryRelationship>
<entryRelationship typeCode="SPRT">
<observation classCode="OBS" moodCode="DEF">
<code code="53037-8" codeSystemName="LOINC" displayName="Genetic disease sequence variation interpretation"/>
<value xsi:type="CD" code="LA6668-3" codeSystemName="LOINC" displayName="Pathogenic"/>
</observation> </entryRelationship> </observation>
Figure 19: Clinical Genomic Statement example