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

ARCHETYPE IDopenEHR-EHR-CLUSTER.copy_number_variant.v0
ConceptGenetic copy number variant
DescriptionDescribes a copy number variant, where any part of a genome was deleted or duplicated (gain or loss of an allele).
UseUse to record the findings for a copy number variant observed in a genetic sequence. This archetype has been specifically designed to be used in the 'Variant' SLOT within the CLUSTER.genetic_variant archetype, but can also be used within other ENTRY or CLUSTER archetypes, where clinically appropriate.
PurposeTo record the details about a copy number variant observed in a genetic sequence.
References
Copyright© openEHR Foundation
AuthorsForfatternavn: Gideon Giacomelli
Organisasjon: Charité Berlin, Germany
E-post: gideon.giacomelli@charite.de
Opprinnelig skrevet dato: 2019-02-01
Other Details LanguageForfatternavn: Gideon Giacomelli
Organisasjon: Charité Berlin, Germany
E-post: gideon.giacomelli@charite.de
Opprinnelig skrevet dato: 2019-02-01
OtherDetails Language Independent{licence=Licence: This work is licensed under the Creative Commons Attribution-ShareAlike 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by-sa/4.0/., custodian_organisation=openEHR Foundation, original_namespace=org.openehr, original_publisher=openEHR Foundation, custodian_namespace=org.openehr, MD5-CAM-1.0.1=23DE86A8320F0CFAABC49A582B946256, build_uid=1a923d95-5002-4c18-88fb-08415aa7edc4, revision=0.0.1-alpha}
Keywords
Lifecyclein_development
UID2af0c3d0-d321-4e33-98f7-e9970379d6a5
Language useden
Citeable Identifier1078.36.2200
Revision Number0.0.1-alpha
AllArchetype [runtimeNameConstraintForConceptName=null, archetypeConceptBinding=null, archetypeConceptDescription=Describes a copy number variant, where any part of a genome was deleted or duplicated (gain or loss of an allele)., archetypeConceptComment=null, otherContributors=Cecilia Mascia, CRS4, Italy
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=ubegrenset, archetypeTranslationTree=null, topLevelToAshis={contacts=[], source=[], ism_transition=[], description=[], protocol=[], credentials=[], target=[], data=[], content=[], other_participations=[], details=[], 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=Valgfritt, 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=Valgfritt, 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=Valgfritt, 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=Valgfritt, 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=Valgfritt, gjentagende, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=Inkluder:
openEHR-EHR-CLUSTER.reference_sequence.v1 og spesialiseringer, extendedValues=null]], relationships=[], activities=[], provider=[], identities=[], state=[], context=[], events=[], capabilities=[]}, topLevelItems={items=ResourceSimplifiedHierarchyItem [path=ROOT_/, code=at0000, itemType=CLUSTER, level=0, text=null, description=null, comment=null, uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Obligatorisk, 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=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=Valgfritt, 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=Valgfritt, 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=Valgfritt, 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=Valgfritt, 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=Valgfritt, gjentagende, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=Inkluder:
openEHR-EHR-CLUSTER.reference_sequence.v1 og spesialiseringer, extendedValues=null]], minIndents={}, termBindingRetrievalErrorMessage=null]