ARCHETYPE Copy number variant (openEHR-EHR-CLUSTER.copy_number_variant.v0)

ARCHETYPE IDopenEHR-EHR-CLUSTER.copy_number_variant.v0
ConceptCopy number variant
DescriptionDescribes a Copy number variant, where any part of a genome was deleted or duplicated (gain or loss of an allele).
UseThis archetype should be used inside the "Variant" SLOT of the "Genetic variant" archetype.
PurposeTo describe a copy number variant observed in a sequence.
References
Copyright© openEHR Foundation
AuthorsAuthor name: Gideon Giacomelli
Organisation: Charité Berlin, Germany
Email: gideon.giacomelli@charite.de
Date originally authored: 2019-02-01
Other Details LanguageAuthor name: Gideon Giacomelli
Organisation: Charité Berlin, Germany
Email: gideon.giacomelli@charite.de
Date originally authored: 2019-02-01
OtherDetails Language Independent{licence=This work is licensed under the Creative Commons Attribution-ShareAlike 3.0 License. To view a copy of this license, visit http://creativecommons.org/licenses/by-sa/3.0/., custodian_organisation=openEHR Foundation, original_namespace=org.openehr, original_publisher=openEHR Foundation, custodian_namespace=org.openehr, MD5-CAM-1.0.1=03B4EDD3924CB29BE7F8A44650DB8C60, build_uid=8e68d88f-0e75-46f4-acdc-1951190f57c8, revision=0.0.1-alpha}
Keywords
Lifecyclein_development
UID2af0c3d0-d321-4e33-98f7-e9970379d6a5
Language useden
Citeable Identifier1013.1.3750
Revision Number0.0.1-alpha
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Christina Jaeger-Schmidt, Heidelberg University Hospital, Germany
Florian Kaercher, Charité Berlin, Germany
Francesca Frexia, CRS4, Italy
Gianluigi Zanetti, CRS4, Italy
Heather Leslie, Atomica Informatics, Australia (openEHR Editor)
Paolo Uva, CRS4, Italy
Silje Ljosland Bakke, Nasjonal IKT HF, Norway (openEHR Editor)
Simon Schumacher, HiGHmed, Germany, originalLanguage=en, translators=, subjectOfData=unconstrained, archetypeTranslationTree=null, topLevelToAshis={details=[], identities=[], source=[], credentials=[], context=[], description=[], ism_transition=[], events=[], content=[], items=[ResourceSimplifiedHierarchyItem [path=/items[at0001], code=at0001, itemType=ELEMENT, level=1, text=Start position, description=Start position on the given reference sequence., comment=Number should not be treated as an absolute more as an estimation., uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_COUNT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0002], code=at0002, itemType=ELEMENT, level=1, text=End position, description=End position on the given reference sequence., comment=Number should not be treated as an absolute more as an estimation., uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_COUNT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0003], code=at0003, itemType=ELEMENT, level=1, text=Total copy number, description=Number of appearance of the allele., comment=null, uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_COUNT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0005], code=at0005, itemType=ELEMENT, level=1, text=Copy number change type, description=Any copy number variant results in a gain or loss of the region e.g. a loss could result that a hetergozygous locus becomes homozygous since one gene was deleted., comment=null, uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_CODED_TEXT, bindings=[LOINC(2.65)::LL1041-4], values=
  • Gain [Copy number gain.]
    [LOINC(2.65)::LA14033-7]
  • Loss [Copy number loss.]
    [LOINC(2.65)::LA14034-5]
, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0004], code=at0004, itemType=SLOT, level=1, text=Reference sequence, description=Structured details about the reference sequence., comment=Should be a specific chromosome most of the time., uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=Include:
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  • Gain [Copy number gain.]
    [LOINC(2.65)::LA14033-7]
  • Loss [Copy number loss.]
    [LOINC(2.65)::LA14034-5]
, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0004], code=at0004, itemType=SLOT, level=1, text=Reference sequence, description=Structured details about the reference sequence., comment=Should be a specific chromosome most of the time., uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=Include:
openEHR-EHR-CLUSTER.Reference_sequence.v0, extendedValues=null]], minIndents={}, termBindingRetrievalErrorMessage=null]