The TestDetailsSection template is the blueprint for all sections describing specific types of genetic testing, such as the genetic variation section, cytogenetic section, etc. It consists of subsections common in genetic testing, e.g., indications, findings, interpretations, specimen, tests performed, and test information. In later releases of the GTR, it could be that specialized sections will be created by extending the TestDetailsSection to represent unique requirements of different types of genetic testing that are not accomodates by TestDetailsSection. The overall structure of TestDetailsSection is depicted in chart 3 of the slide deck enclosed in the GTR package.
Context
Parent nodes of template element with id 2.16.840.1.113883.10.20.20.1.8
Classification
CDA Section Level Template
Open/Closed
Open (other than defined elements are allowed)
Used by / Uses
Used by 1 transaction and 1 template, Uses 7 templates
<section> <templateIdroot="2.16.840.1.113883.10.20.20.1.8"/><title>Genetic Variations</title><entry> <observationclassCode="OBS"moodCode="EVN"> <templateIdroot="2.16.840.1.113883.10.20.20.2.1"/><idroot="2.16.840.1.113883.18.12.7.30.9.8.1"/><codecode="55208-3"codeSystemName="LOINC"displayName="DNA Analysis Discrete Sequence Variant Panel"/><statusCodecode="completed"/><effectiveTimevalue="200512011500"/><entryRelationshiptypeCode="SUBJ"> <observationclassCode="OBS"moodCode="EVN"> <idroot="2.16.840.1.113883.18.12.7.30.9.3.7"/><code/></observation></entryRelationship><entryRelationshiptypeCode="SUBJ"> <observationclassCode="OBS"moodCode="EVN"> <templateIdroot="2.16.840.1.113883.10.20.20.2.1.5"/><codecode="48018-6"codeSystemName="LOINC"displayName="Gene Identifier"/><valuexsi:type="CD"code="GJB2"codeSystemName="HGNC"/></observation></entryRelationship><entryRelationshiptypeCode="SUBJ"> <observationclassCode="OBS"moodCode="EVN"> <templateIdroot="2.16.840.1.113883.10.20.20.2.1.8"/><codecode="48013-7"codeSystemName="LOINC"displayName="Genomic Reference Sequence Identifier"/><valuexsi:type="CD"code="NC_000013.10"codeSystem="REFSEQ"codeSystemName="NCBI Reference Sequence"/></observation></entryRelationship><entryRelationshiptypeCode="SUBJ"> <observationclassCode="OBS"moodCode="EVN"> <templateIdroot="2.16.840.1.113883.10.20.20.2.1.6"/><codecode="51958-7"codeSystemName="LOINC"displayName="Transcript Reference Sequence Identifier"/><valuexsi:type="CD"code="NM_004004.5"codeSystem="REFSEQ"codeSystemName="NCBI Reference Sequence"/></observation></entryRelationship><entryRelationshiptypeCode="SUBJ"> <observationclassCode="OBS"moodCode="EVN"> <templateIdroot="2.16.840.1.113883.10.20.20.2.1.7"/><codecode="48003-8"codeSystemName="LOINC"displayName="DNA Sequence Variation Identifier"/><valuexsi:type="CD"code="rs72474224"codeSystemName="dbSNP"/></observation></entryRelationship><entryRelationshiptypeCode="SUBJ"> <observationclassCode="OBS"moodCode="EVN"> <templateIdroot="2.16.840.1.113883.10.20.20.2.1.2"/><codecode="48004-6"codeSystemName="LOINC"displayName="DNA Sequence Variation"/><valuexsi:type="CD"code="109G>A"codeSystemName="HGVS nomenclature for the description of sequence variations"/></observation></entryRelationship><entryRelationshiptypeCode="SUBJ"> <observationclassCode="OBS"moodCode="EVN"> <templateIdroot="2.16.840.1.113883.10.20.20.2.1.2.1"/><codecode="48019-4"codeSystemName="LOINC"displayName="DNA Sequence Variation Type"/><valuexsi:type="CD"code="LA6690-7"codeSystemName="LOINC"displayName="Substitution"/></observation></entryRelationship><entryRelationshiptypeCode="SUBJ"> <observationclassCode="OBS"moodCode="EVN"> <templateIdroot="2.16.840.1.113883.10.20.20.2.1.1"/><codecode="48005-3"codeSystemName="LOINC"displayName="Amino Acid Change"/><valuexsi:type="CD"code="Val37Ile"/></observation></entryRelationship><entryRelationshiptypeCode="SUBJ"> <observationclassCode="OBS"moodCode="EVN"> <templateIdroot="2.16.840.1.113883.10.20.20.2.1.1.1"/><codecode="48006-1"codeSystemName="LOINC"displayName="Amino acid change type"/><valuexsi:type="CD"code="LA6698-0"displayName="Missense"/></observation></entryRelationship><entryRelationshiptypeCode="SUBJ"> <observationclassCode="OBS"moodCode="EVN"> <templateIdroot="2.16.840.1.113883.10.20.20.2.1.3"/><codecode="47999-8"codeSystemName="LOINC"displayName="DNA Region Name"/><valuexsi:type="ST">Exon 2</value></observation></entryRelationship><entryRelationshiptypeCode="SUBJ"> <observationclassCode="OBS"moodCode="EVN"> <templateIdroot="2.16.840.1.113883.10.20.20.2.1.4"/><codecode="53034-5"codeSystemName="LOINC"displayName=" Allelic State"/><valuexsi:type="CD"code="LA6705-3"codeSystemName="LOINC"displayName="Homozygous"/></observation></entryRelationship><entryRelationshiptypeCode="RSON"> <observationclassCode="OBS"moodCode="EVN"> <idroot="2.16.840.1.113883.18.12.7.30.9.2.1"/><code/></observation></entryRelationship><entryRelationshiptypeCode="SPRT"> <observationclassCode="OBS"moodCode="DEF"> <templateIdroot="2.16.840.1.113883.10.20.20.2.5.3"/><codecode="53037-8"codeSystemName="LOINC"displayName="Genetic disease sequence variation interpretation"/><valuexsi:type="CD"code="LA6668-3"codeSystemName="LOINC"displayName="Pathogenic"/></observation></entryRelationship></observation></entry><entry> <observationclassCode="OBS"moodCode="EVN"> <templateIdroot="2.16.840.1.113883.10.20.20.2.1"/><idroot="2.16.840.1.113883.18.12.7.30.9.8.2"/><codecode="55208-3"codeSystemName="LOINC"displayName=" DNA Analysis Discrete Sequence Variant Panel"/><statusCodecode="completed"/><effectiveTimevalue="200512011500"/><entryRelationshiptypeCode="SUBJ"> <observationclassCode="OBS"moodCode="EVN"> <idroot="2.16.840.1.113883.18.12.7.30.9.3.7"/><code/></observation></entryRelationship><entryRelationshiptypeCode="SUBJ"> <observationclassCode="OBS"moodCode="EVN"> <codecode="48018-6"codeSystemName="LOINC"displayName="Gene Identifier"/><valuexsi:type="CD"code="GJB2"codeSystemName="HUGO"/></observation></entryRelationship><entryRelationshiptypeCode="SUBJ"> <observationclassCode="OBS"moodCode="EVN"> <codecode="51958-7"codeSystemName="LOINC"displayName="Transcript Reference Sequence Identifier"/><valuexsi:type="CD"code="NM_004004.5"codeSystem="REFSEQ"codeSystemName="NCBI Reference Sequence"/></observation></entryRelationship><entryRelationshiptypeCode="SUBJ"> <observationclassCode="OBS"moodCode="EVN"> <codecode="48003-8"codeSystemName="LOINC"displayName="DNA Sequence Variation Identifier"/><valuexsi:type="CD"code="rs2274084"codeSystemName="dbSNP"/></observation></entryRelationship><entryRelationshiptypeCode="SUBJ"> <observationclassCode="OBS"moodCode="EVN"> <codecode="48004-6"codeSystemName="LOINC"displayName="DNA Sequence Variation"/><valuexsi:type="CD"code="79G>A"codeSystemName="HGVS nomenclature for the description of sequence variations"/></observation></entryRelationship><entryRelationshiptypeCode="SUBJ"> <observationclassCode="OBS"moodCode="EVN"> <codecode="48019-4"codeSystemName="LOINC"displayName="DNA Sequence Variation Type"/><valuexsi:type="CD"code="LA6690-7"codeSystemName="LOINC"displayName="Substitution"/></observation></entryRelationship><entryRelationshiptypeCode="SUBJ"> <observationclassCode="OBS"moodCode="EVN"> <codecode="48005-3"codeSystemName="LOINC"displayName="Amino Acid Change"/><valuexsi:type="CD"code="Val27Ile"/></observation></entryRelationship><entryRelationshiptypeCode="SUBJ"> <observationclassCode="OBS"moodCode="EVN"> <codecode="48006-1"codeSystemName="LOINC"displayName="Amino acid change type"/><valuexsi:type="CD"code="LA6698-0"displayName="Missense"/></observation></entryRelationship><entryRelationshiptypeCode="SUBJ"> <observationclassCode="OBS"moodCode="EVN"> <codecode="47999-8"codeSystemName="LOINC"displayName="DNA Region Name"/><valuexsi:type="ST">Exon 2</value></observation></entryRelationship><entryRelationshiptypeCode="SUBJ"> <observationclassCode="OBS"moodCode="EVN"> <codecode="53034-5"codeSystemName="LOINC"displayName=" Allelic State"/><valuexsi:type="CD"code="LA6706-1"codeSystemName="LOINC"displayName="Heterozygous"/></observation></entryRelationship><entryRelationshiptypeCode="RSON"> <observationclassCode="OBS"moodCode="EVN"> <idroot="2.16.840.1.113883.18.12.7.30.9.2.1"/><code/></observation></entryRelationship><entryRelationshiptypeCode="SPRT"> <observationclassCode="OBS"moodCode="DEF"> <templateIdroot="2.16.840.1.113883.10.20.20.2.5.3"/><codecode="53037-8"codeSystemName="LOINC"displayName="Genetic disease sequence variation interpretation"/><valuexsi:type="CD"code="LA6675-8"codeSystemName="LOINC"displayName="Benign"/></observation></entryRelationship></observation></entry><component> <section> <templateIdroot="2.16.840.1.113883.10.20.20.1.10"/><title>Tests Performed</title><text> <list> <item> <content> GJB2 Full Gene Test </content></item></list></text><entry> <observationclassCode="OBS"moodCode="EVN"> <templateIdroot="2.16.840.1.113883.10.20.20.3.4"/><codedisplayName="Test Performed"/><statusCodecode="completed"/><effectiveTimevalue="200512011500"/><valuexsi:type="CD"code="CX26FULL"codeSystem="2.16.840.1.113883.6.1"codeSystemName="LOINC"displayName="Connexin 26 Full Gene Test"> <originalText> <referencevalue="#a1"/></originalText></value><entryRelationshiptypeCode="RSON"> <observationclassCode="COND"moodCode="EVN"> <idroot="2.16.840.1.113883.18.12.7.30.9.2.1"/><code/></observation></entryRelationship></observation></entry></section></component><component> <section> <templateIdroot="2.16.840.1.113883.10.20.20.1.12"/><title>Findings</title><text> <list> <item> <content> DNA MUTATIONS: Heterozygous 109G>A (V37I), Exon 2, GJB2 </content></item><item> <content> INCIDENTAL VARIANTS: Heterozygous 79G>A (V27I), Exon 2, GJB2 </content></item></list></text></section></component><component> <section> <templateIdroot="2.16.840.1.113883.10.20.20.1.13"/><title>Interpretation</title><text> <list> <item> <content>Mutations interpretation</content><list> <item> <content>V37I - Pathogenic</content></item><item> <content>V27I - Benign</content></item></list></item><item> <content> Details: DNA sequencing detected two mutations in the GJB2 gene, 79G>A (V27I) and 109G>A (V37I). The V27I mutation has been reported as a benign variant (references) and is not believed to cause hearing loss. The V37I mutation has been previously reported in patients with hearing loss. This mutation, in homozygosity or combined with another GJB2 disease causing mutation, typically results in a mild to moderate hearing loss (Cryns et al. 2005). Mutations in both copies of the GJB2 gene are necessary to assume that GJB2 is responsible for the hearing loss. Although two mutations were identified in this patient, we would assume that the combination of a benign variant and a mild pathogenic mutation would result in a mild to moderate hearing loss rather than a moderately-severe one, as in this patient. It is most likely that the hearing loss in this patient is the result of the V37I mutation and an unknown second pathogenic mutation. It should be noted that a second mutation is not identified in a large percentage (10-50%) of patients with nonsyndromic hearing loss and GJB2 mutations (del Castillo et al. 2003). </content></item></list></text></section></component></section>
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Description
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hl7:section
Testtion
Constraint
Sub-sections of the TestDetailsSection SHOULD appear in the order presented in this implementation guide.