2.16.840.1.113883.10.20.20.2

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Template ClinicalGenomicStatement

Aktuelle Version

Id	2.16.840.1.113883.10.20.20.2 ref gtr-	Gültigkeit	2013‑02‑01
Status	Entwurf	Versions-Label
Name	ClinicalGenomicStatement	Bezeichnung	Clinical Genomic Statement
Beschreibung The ClinicalGenomicStatement (CGS) template is the main vehicle of representing structured data in the GTR Implementation Guide. At its core, there is a genetic observation finding (result), e.g., a genetic variation, which can be associated with the following: more observations that describe the core observation in more detail (GenomicAssociatedObservation), e.g., amino acid change type; indications for performing this genetic observation (IndicationObservation), e.g., the genetic disease being assessed; and interpretations of the observation finding (InterpretivePhenotype), e.g., the mutation is pathogenic. In addition, it is important to associate a specimen and genomic source class with the core genetic finding, and optionally other performers of the genetic observation or the interpretation than those listed in the GTR header could be specified as part the CGS template. The overall structure of CGS is depicted in chart 5 of the slide deck enclosed in the GTR package. 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. The latter is constrained by several of its sub-templates in order to suggest binding to LOINC value sets describing interpretations of genetic testing. For example, ClinicalGenomicStatementGeneticVariation is a sub-template of ClinicalGenomicStatement and is associated with InterpretivePhenotypeGeneticVariation which is a sub-template of InterpretivePhenotype and its code and value attributes may be bound to LOINC codes representing interpretations of genetic findings. All GTR structured data entries shall be part of CGS instances so that parsing applications can find the full semantics explicitly represented in this single and coherent structure. Sub-sections such as Indications, Interpretations and Specimen are mainly for presenting the data for human viewing (narrative), but they may also contain structured data that shall reference or be referenced from CGS. By using the referencing mechanism (explained in the GenomicObservationReference template), 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. Note that CGS structured entries may point to the respective narrative in sub-sections by means of XML ID (see examples in the GTR samples enclosed in the GTR package). This mechanism can be useful in cases where the structured data has been generated by automated processes rather than by human coders.
Kontext	Elternknoten des Template-Element mit Id 2.16.840.1.113883.10.20.20.2
Klassifikation	CDA Entry Level Template
Offen/Geschlossen	Offen (auch andere als die definierten Elemente sind erlaubt)
Benutzt	Benutzt 4 Templates Benutzt als Name Version 2.16.840.1.113883.10.20.20.3.3 Containment Indication Observation DYNAMIC 2.16.840.1.113883.10.20.20.2.5 Containment Interpretive Phenotype DYNAMIC 2.16.840.1.113883.10.20.20.3.2 Containment Genomic Source Class DYNAMIC 2.16.840.1.113883.10.20.20.4 Containment Genomic Associated Observation DYNAMIC
Beispiel	Beispiel <observation 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">       <id root="2.16.840.1.113883.18.12.7.30.9.3.7"/>      <code/>    </observation>  </entryRelationship>  <entryRelationship typeCode="SUBJ">     <observation classCode="OBS" moodCode="EVN">       <templateId root="2.16.840.1.113883.10.20.20.2.1.5"/>      <code code="48018-6" codeSystemName="LOINC" displayName="Gene Identifier"/>      <value xsi:type="CD" code="GJB2" codeSystemName="HGNC"/>    </observation>  </entryRelationship>  <entryRelationship typeCode="SUBJ">     <observation classCode="OBS" moodCode="EVN">       <templateId root="2.16.840.1.113883.10.20.20.2.1.8"/>      <code code="48013-7" codeSystemName="LOINC" displayName="Genomic Reference Sequence Identifier"/>      <value xsi:type="CD" code="NC_000013.10" codeSystem="REFSEQ" codeSystemName="NCBI Reference Sequence"/>    </observation>  </entryRelationship>  <entryRelationship typeCode="SUBJ">     <observation classCode="OBS" moodCode="EVN">       <templateId root="2.16.840.1.113883.10.20.20.2.1.6"/>      <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">       <templateId root="2.16.840.1.113883.10.20.20.2.1.7"/>      <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">       <templateId root="2.16.840.1.113883.10.20.20.2.1.2"/>      <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">       <templateId root="2.16.840.1.113883.10.20.20.2.1.2.1"/>      <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">       <templateId root="2.16.840.1.113883.10.20.20.2.1.1.1"/>      <code code="48006-1" codeSystemName="LOINC" displayName="Amino acid change type"/>      <value xsi:type="CD" code="LA6698-0" displayName="Missense"/>    </observation>  </entryRelationship>  <entryRelationship typeCode="SUBJ">     <observation classCode="OBS" moodCode="EVN">       <templateId root="2.16.840.1.113883.10.20.20.2.1.3"/>      <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">       <templateId root="2.16.840.1.113883.10.20.20.2.1.4"/>      <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">       <templateId root="2.16.840.1.113883.10.20.20.2.5.3"/>      <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>
Item DT Kard Konf Beschreibung Label hl7:observation (Cli...ent) hl7:templateId II 1 … 1 M (Cli...ent) @root uid 1 … 1 F 2.16.840.1.113883.10.20.20.2 hl7:code 1 … 1 R The code attribute of a clinical genomic statement characterizes the type of data it represents (e.g., genetic variation) and specifically it indicates the type of information assigned to the value attribute of that clinical genomic statement. (Cli...ent) hl7:value 0 … 1 (Cli...ent) hl7:entryRelationship 1 … 1 R Indication Observation Beinhaltet 2.16.840.1.113883.10.20.20.3.3 Indication Observation (DYNAMIC) (Cli...ent) @typeCode cs 1 … 1 F RSON hl7:entryRelationship 0 … 1 R Interpretive Phenotype Beinhaltet 2.16.840.1.113883.10.20.20.2.5 Interpretive Phenotype (DYNAMIC) (Cli...ent) @typeCode cs 1 … 1 F SPRT hl7:entryRelationship 0 … 1 R Genomic Source Class Beinhaltet 2.16.840.1.113883.10.20.20.3.2 Genomic Source Class (DYNAMIC) (Cli...ent) @typeCode cs 1 … 1 F SUBJ hl7:performer 0 … * Use this performer association if the performer(s) of the genomic observation (i.e., the source of this performer association) are different than the performer(s) indicated at a higher level (e.g., the GTR header). (Cli...ent)   Constraint Contains exactly one [1..1] CDA Performer2 hl7:entryRelationship 1 … 1 R Genomic Associated Observation Beinhaltet 2.16.840.1.113883.10.20.20.4 Genomic Associated Observation (DYNAMIC) (Cli...ent) @typeCode cs 1 … 1 F SUBJ

Zusammenstellung aller Versionen dieses Templates

• 2013-02-01 (In Entwicklung)