[Observation: templateId 2.16.840.1.113883.10.20.20.2.1]
The ClinicalGenomicStatementGeneticVariation template is a sub-template of ClinicalGenomicStatement. It is used by TestDetailsSection to carry the structured data that is unique to genetic variations. It is associated with InterpretivePhenotypeObservation sub-templates.
1. SHALL conform to Clinical Genomic Statement template (templateId: 2.16.840.1.113883.10.20.20.2) 2. SHALL contain exactly one [1..1] code (CONF-GTR-90)
• In principle, the code attribute should designate the type of the genetic variation being described in this Clinical Genomic Statement. Typically, a genetic variation can be characterized by multiple aspects, e.g., DNA change, amino acid change, Transcript Reference Sequence Identifier, etc. It is important to note that
there is no single standard for any type of genetic variation and even HGVS nomenclature doesn't cover all cases. Also, 'gene-centric' variation notations might be disadvantageous because in some genomic locations, a variant may be influencing several genes (or transcripts of the same gene) and may have different effects, for example, an indel in an intron of one transcript may be a frame shift in an exon another transcript for the same gene.
When possible, a coded panel of such characteristics should be used, for example, the LOINC panel "DNA Analysis Discrete Sequence Variant Panel" (code=55208-3) designed for clinical environment. When this code is assigned to the code attribute, then this Clinical Genomic Statement SHALL consist of nesting observations describing the Gene Identifier, Transcript Reference Sequence Identifier, DNA Sequence Variation, DNA Sequence Variation Type, Amino Acid Change, Amino Acid Change Type, DNA Region Name, Allelic State, Genomic Source Class. The constraining of these nesting observations are described in detail in the associations of this Clinical Genomic Statement, including their code and binding value sets.
If code is not assigned with the above-mentioned LOINC Panel, then it should use either the Human Genome Variation Society (HGVS) nomenclature (identified as HGNC with OID = 2.16.840.1.113883.6.281) or other recognized notation of genetic variations (TBD).
3. SHOULD contain zero or one [0..1] value (CONF-GTR-55) • Please refer to the code attribute documentation.
a. If code=55208-3 (LOINC code for "DNA Analysis Discrete Sequence Variant Panel"), then value SHALL NOT be used. (CONF-GTR-91)
4. MAY contain zero or one [0..1] entryRelationship
a. Contains @typeCode="COMP" COMP
b. Contains exactly one [1..1] Interpretive Phenotype Genetic Variation (templateId:
2.16.840.1.113883.10.20.20.2.5.3) 5. MAY contain zero or one [0..1] entryRelationship
a. Contains @typeCode="COMP" COMP
b. Contains exactly one [1..1] Interpretive Phenotype Pharmacogenomic Drug Efficacy (templateId:
2.16.840.1.113883.10.20.20.2.5.4.1) 6. MAY contain zero or one [0..1] entryRelationship
a. Contains @typeCode="COMP" COMP
b. Contains exactly one [1..1] Interpretive Phenotype Pharmacogenomic Drug Metabolism (templateId:
2.16.840.1.113883.10.20.20.2.5.4.2) 7. SHOULD contain zero or one [0..1] entryRelationship
a. Contains exactly one [1..1] Genetic Variation Associated Observation Amino Acid Change (templateId:
2.16.840.1.113883.10.20.20.2.1.1)
8. SHOULD contain zero or one [0..1] entryRelationship
a. Contains exactly one [1..1] Genetic Variation Associated Observation DNA Change (templateId:
2.16.840.1.113883.10.20.20.2.1.2)
9. SHOULD contain zero or one [0..1] entryRelationship
a. Contains exactly one [1..1] Genetic Variation Associated Observation DNA Region Name (templateId:
2.16.840.1.113883.10.20.20.2.1.3)
10. SHOULD contain zero or one [0..1] entryRelationship
a. Contains exactly one [1..1] Genetic Variation Associated Observation Zygosity (templateId:
2.16.840.1.113883.10.20.20.2.1.4)
1. SHALL conform to Clinical Genomic Statement template (templateId: 2.16.840.1.113883.10.20.20.2) 2. Contains exactly one [1..1] @classCode with data type ActClassObservation
3. Contains exactly one [1..1] @moodCode with data type x_ActMoodDocumentObservation 4. SHALL contain exactly one [1..1] code (CONF-GTR-90)
• In principle, the code attribute should designate the type of the genetic variation being described in this Clinical Genomic Statement. Typically, a genetic variation can be characterized by multiple aspects, e.g., DNA change, amino acid change, Transcript Reference Sequence Identifier, etc. It is important to note that there is no single standard for any type of genetic variation and even HGVS nomenclature doesn't cover all cases. Also, 'gene-centric' variation notations might be disadvantageous because in some genomic locations, a variant may be influencing several genes (or transcripts of the same gene) and may have different effects, for example, an indel in an intron of one transcript may be a frame shift in an exon another transcript for the same gene.
When possible, a coded panel of such characteristics should be used, for example, the LOINC panel "DNA Analysis Discrete Sequence Variant Panel" (code=55208-3) designed for clinical environment. When this code is assigned to the code attribute, then this Clinical Genomic Statement SHALL consist of nesting observations describing the Gene Identifier, Transcript Reference Sequence Identifier, DNA Sequence Variation, DNA Sequence Variation Type, Amino Acid Change, Amino Acid Change Type, DNA Region Name, Allelic State, Genomic Source Class. The constraining of these nesting observations are described in detail in the associations of this Clinical Genomic Statement, including their code and binding value sets.
If code is not assigned with the above-mentioned LOINC Panel, then it should use either the Human Genome Variation Society (HGVS) nomenclature (identified as HGNC with OID = 2.16.840.1.113883.6.281) or other recognized notation of genetic variations (TBD).
5. SHOULD contain zero or one [0..1] value (CONF-GTR-55)
a. If code=55208-3 (LOINC code for "DNA Analysis Discrete Sequence Variant Panel"), then value SHALL NOT be used. (CONF-GTR-91)
• Please refer to the code attribute documentation.
6. 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) 7. 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) 8. MAY contain zero or one [0..1] entryRelationship
a. Contains @typeCode="COMP" COMP
b. Contains exactly one [1..1] Interpretive Phenotype Genetic Variation (templateId:
2.16.840.1.113883.10.20.20.2.5.3) 9. MAY contain zero or one [0..1] entryRelationship
a. Contains @typeCode="COMP" COMP
b. Contains exactly one [1..1] Interpretive Phenotype Pharmacogenomic Drug Efficacy (templateId:
2.16.840.1.113883.10.20.20.2.5.4.1) 10. MAY contain zero or one [0..1] entryRelationship
a. Contains @typeCode="COMP" COMP
b. Contains exactly one [1..1] Interpretive Phenotype Pharmacogenomic Drug Metabolism (templateId:
2.16.840.1.113883.10.20.20.2.5.4.2) 11. SHOULD contain zero or one [0..1] entryRelationship
a. Contains exactly one [1..1] Genetic Variation Associated Observation Amino Acid Change (templateId:
2.16.840.1.113883.10.20.20.2.1.1)
12. SHOULD contain zero or one [0..1] entryRelationship
a. Contains exactly one [1..1] Genetic Variation Associated Observation DNA Change (templateId:
2.16.840.1.113883.10.20.20.2.1.2)
a. Contains exactly one [1..1] Genetic Variation Associated Observation DNA Region Name (templateId:
2.16.840.1.113883.10.20.20.2.1.3)
14. SHOULD contain zero or one [0..1] entryRelationship
a. Contains exactly one [1..1] Genetic Variation Associated Observation Zygosity (templateId:
2.16.840.1.113883.10.20.20.2.1.4)
15. If code=55208-3 (LOINC code for "DNA Analysis Discrete Sequence Variant Panel"), then value SHALL NOT be used. (CONF-GTR-91)
<?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"/>
<value xsi:type="CD" code="LA6698-0" displayName="Missense"/> </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 22: Clinical Genomic Statement Genetic Variation example