ARCHETYPE Sequencing assay (openEHR-EHR-CLUSTER.sequencing_assay.v0)

ARCHETYPE IDopenEHR-EHR-CLUSTER.sequencing_assay.v0
ConceptSequencing assay
DescriptionTo record details of the sequencing analysis including a list of all tested genes if panel sequencing was performed.
UseOne or more instances of this archetype may be nested within the 'Testing details' SLOT in the OBSERVATION.laboratory_test_result.
PurposeTo record details of the performed sequencing analysis including a list of all tested genes if panel sequencing was performed.
References
Copyright© openEHR Foundation
AuthorsAuthor name: Aurelie Tomczak
Organisation: Institute of Pathology, University Hospital Heidelberg
Email: au.tomczak@yahoo.com
Date originally authored: 2019-06-24
Other Details LanguageAuthor name: Aurelie Tomczak
Organisation: Institute of Pathology, University Hospital Heidelberg
Email: au.tomczak@yahoo.com
Date originally authored: 2019-06-24
OtherDetails Language Independent{custodian_organisation=HiGHmed, original_namespace=org.highmed, original_publisher=HiGHmed, custodian_namespace=org.highmed, MD5-CAM-1.0.1=F87973FA993393492F3A69851462F782, build_uid=b7b893d9-11c7-47d6-a7cf-a86c096edadb, revision=0.0.1-alpha}
KeywordsSequencing, Genomics, Panel, Assay, Pathology
Lifecyclein_development
UIDe0c0ce17-d41c-4eed-8cfb-2f863e531daf
Language useden
Citeable Identifier1246.145.506
Revision Number0.0.1-alpha
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, subjectOfData=unconstrained, archetypeTranslationTree=null, topLevelToAshis={relationships=[], identities=[], provider=[], content=[], events=[], data=[], credentials=[], capabilities=[], target=[], items=[ResourceSimplifiedHierarchyItem [path=/items[at0001], code=at0001, itemType=ELEMENT, level=1, text=Sequencing technology, description=Name of the technology used for sequencing analysis., comment=null, uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CHOICE, bindings=null, values=Choice of:
  •  Coded Text
    • NGS (hybrid-capture) [*]
    • NGS (amplicon) [*]
    • Genome sequencing [*]
    • Array-CGH [*]
    • MLPA [*]
    • Sanger sequencing [*]
    • Fragment analysis [*]
    • Methylation assay [*]
    • miscellaneous [*]
  •  Text
, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0002], code=at0002, itemType=ELEMENT, level=1, text=Kit name, description=Name of the kit used for the experiment., comment=null, uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CHOICE, bindings=null, values=Choice of:
  •  Text
  •  Coded Text
    • Oncomine Comprehensive Panel V3 [*]
, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0003], code=at0003, itemType=ELEMENT, level=1, text=Nucleic acid, description=Type of nucleic acid used for sequencing, e.g. DNA, RNA oder cf-DNA., comment=null, uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CHOICE, bindings=null, values=Choice of:
  •  Text
  •  Coded Text
    • DNA [*]
    • RNA [*]
    • cf-DNA [*]
, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0020], code=at0020, itemType=ELEMENT, level=1, text=Tumor cell percentage, description=To record the tumor cell content in percent., comment=null, uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_COUNT, bindings=null, values=min: >=0; max: <=100

, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0026], code=at0026, itemType=SLOT, level=1, text=Extensions, description=Additional details to be captured, comment=null, uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=Include:
All not explicitly excluded archetypes, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0006], code=at0006, itemType=CLUSTER, level=1, text=Tested Genes, description=List of all tested genes, if panel sequencing was performed., comment=null, uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=1..*, cardinalityText=, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0006]/items[at0007], code=at0007, itemType=ELEMENT, level=2, text=Gen symbol, description=The official gene symbol approved by the HGNC, which is a short abbreviated form of the gene name., comment=null, uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0006]/items[at0008], code=at0008, itemType=ELEMENT, level=2, text=Gen name, description=The full gene name approved by the HGNC that convey the character or function of the gene., comment=null, uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0006]/items[at0025], code=at0025, itemType=SLOT, level=2, text=Gene reference sequence, description=Structured details about the gene reference sequence., comment=null, uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=Include:
.* Or
openEHR-EHR-CLUSTER.reference_sequence.v1, extendedValues=null]], protocol=[], ism_transition=[], contacts=[], activities=[], context=[], other_participations=[], state=[], details=[], description=[], source=[]}, topLevelItems={items=ResourceSimplifiedHierarchyItem [path=ROOT_/, code=at0000, itemType=CLUSTER, level=0, text=null, description=null, comment=null, uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=1..*, cardinalityText=, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=null, extendedValues=null]}, addHierarchyItemsTo=items, currentHierarchyItemsForAdding=[ResourceSimplifiedHierarchyItem [path=/items[at0001], code=at0001, itemType=ELEMENT, level=1, text=Sequencing technology, description=Name of the technology used for sequencing analysis., comment=null, uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CHOICE, bindings=null, values=Choice of:
  •  Coded Text
    • NGS (hybrid-capture) [*]
    • NGS (amplicon) [*]
    • Genome sequencing [*]
    • Array-CGH [*]
    • MLPA [*]
    • Sanger sequencing [*]
    • Fragment analysis [*]
    • Methylation assay [*]
    • miscellaneous [*]
  •  Text
, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0002], code=at0002, itemType=ELEMENT, level=1, text=Kit name, description=Name of the kit used for the experiment., comment=null, uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CHOICE, bindings=null, values=Choice of:
  •  Text
  •  Coded Text
    • Oncomine Comprehensive Panel V3 [*]
, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0003], code=at0003, itemType=ELEMENT, level=1, text=Nucleic acid, description=Type of nucleic acid used for sequencing, e.g. DNA, RNA oder cf-DNA., comment=null, uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CHOICE, bindings=null, values=Choice of:
  •  Text
  •  Coded Text
    • DNA [*]
    • RNA [*]
    • cf-DNA [*]
, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0020], code=at0020, itemType=ELEMENT, level=1, text=Tumor cell percentage, description=To record the tumor cell content in percent., comment=null, uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_COUNT, bindings=null, values=min: >=0; max: <=100

, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0026], code=at0026, itemType=SLOT, level=1, text=Extensions, description=Additional details to be captured, comment=null, uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=Include:
All not explicitly excluded archetypes, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0006], code=at0006, itemType=CLUSTER, level=1, text=Tested Genes, description=List of all tested genes, if panel sequencing was performed., comment=null, uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=1..*, cardinalityText=, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0006]/items[at0007], code=at0007, itemType=ELEMENT, level=2, text=Gen symbol, description=The official gene symbol approved by the HGNC, which is a short abbreviated form of the gene name., comment=null, uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0006]/items[at0008], code=at0008, itemType=ELEMENT, level=2, text=Gen name, description=The full gene name approved by the HGNC that convey the character or function of the gene., comment=null, uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0006]/items[at0025], code=at0025, itemType=SLOT, level=2, text=Gene reference sequence, description=Structured details about the gene reference sequence., comment=null, uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=Include:
.* Or
openEHR-EHR-CLUSTER.reference_sequence.v1, extendedValues=null]], minIndents={}, termBindingRetrievalErrorMessage=null]