ARCHETYPE Genomic copy number variant (openEHR-EHR-CLUSTER.genomic_copy_number_variant.v0)

ARCHETYPE IDopenEHR-EHR-CLUSTER.genomic_copy_number_variant.v0
ConceptGenomic copy number variant
DescriptionA human genetic sequence change where, compared to a genomic reference sequence, a DNA segment, that is 1 kilobases (kb) or larger, was deleted or duplicated.
UseUse to record the details about a copy number variant of human DNA, observed in a genomic sequence. This archetype has been specifically designed to be used in the 'Structured variant' SLOT within the CLUSTER.genetic_variant archetype, but can also be used within other ENTRY or CLUSTER archetypes, where clinically appropriate.
MisuseNot to be used to record information about variants of non-human DNA, or any kind of RNA or protein. Not to be used to record a change where the size of the DNA segment is shorter than 1kb. Use the CLUSTER.repeated_sequence_variant archetype for this purpose.
PurposeTo record the details about a copy number variant of human DNA, observed in a genomic 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 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=EC5F4721BF47A25438632BB7F6083388, build_uid=078d3313-bcda-4f6f-b737-1d47f20dd869, revision=0.0.1-alpha}
Keywordscopy number, variation, genetic, genomic
Lifecyclein_development
UID0b1e5145-b0fd-4844-ae78-5a102fed7928
Language useden
Citeable Identifier1246.145.738
Revision Number0.0.1-alpha
AllArchetype [runtimeNameConstraintForConceptName=null, archetypeConceptBinding=null, archetypeConceptDescription=A human genetic sequence change where, compared to a genomic reference sequence, a DNA segment, that is 1 kilobases (kb) or larger, was deleted or duplicated., 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
Gunnar Houge, Haukeland University Hospital, Norway
Gyri Aasland Gradek, Haukeland University Hospital, Norway
Asbjørg Stray-Pedersen, Oslo University Hospital, Norway
Toril Fagerheim, University Hospital of North Norway, Norway
Camilla F. Skjelbred, Telemark HF Hospital, Norway
Dag Erik Undlien, Oslo University Hospital, Norway
Rune Østern, St Olavs Hospital, Norway, originalLanguage=en, translators=German: Aurelie Tomczak, Institute of Pathology, University Hospital Heidelberg, Germany, au.tomczak@yahoo.com
Norwegian Bokmål: Liv Laugen, ​Oslo University Hospital, Norway, liv.laugen@ous-hf.no
, subjectOfData=unconstrained, archetypeTranslationTree=null, topLevelToAshis={events=[], source=[], contacts=[], content=[], details=[], description=[], ism_transition=[], provider=[], activities=[], target=[], identities=[], data=[], state=[], other_participations=[], capabilities=[], context=[], credentials=[], items=[ResourceSimplifiedHierarchyItem [path=/items[at0001], code=at0001, itemType=ELEMENT, level=1, text=Start, description=Position or range of possible positions of the first nucleotide of the CNV., comment=null, uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CHOICE, bindings=null, values=Choice of:
  •  Count
  •  Interval of Count


, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0002], code=at0002, itemType=ELEMENT, level=1, text=End, description=Position or range of possible positions of the last nucleotide of the CNV., comment=null, uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CHOICE, bindings=null, values=Choice of:
  •  Count
  •  Interval of Count


, 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=min: >1

, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0005], code=at0005, itemType=ELEMENT, level=1, text=Copy number change type, description=Type of sequence alteration., comment=Different type of impact, such as low-level amplification or whole gene deletion, should be recorded using the Reported impact Cluster within the CLUSTER.genetic_variant.v0 archetype., uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_CODED_TEXT, bindings=null, values=
  • Gain [A sequence alteration whereby the copy number of a given region is greater than the reference sequence.]
  • Loss [A sequence alteration whereby the copy number of a given region is less than the reference sequence.]
, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0004], code=at0004, itemType=SLOT, level=1, text=Reference sequence, description=The sequence file used as a reference to describe this variant., 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.v1 and specialisations, extendedValues=null]], protocol=[], relationships=[]}, topLevelItems={items=ResourceSimplifiedHierarchyItem [path=ROOT_/, code=at0000, itemType=CLUSTER, level=0, text=null, description=null, comment=null, uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, 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, description=Position or range of possible positions of the first nucleotide of the CNV., comment=null, uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CHOICE, bindings=null, values=Choice of:
  •  Count
  •  Interval of Count


, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0002], code=at0002, itemType=ELEMENT, level=1, text=End, description=Position or range of possible positions of the last nucleotide of the CNV., comment=null, uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CHOICE, bindings=null, values=Choice of:
  •  Count
  •  Interval of Count


, 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=min: >1

, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0005], code=at0005, itemType=ELEMENT, level=1, text=Copy number change type, description=Type of sequence alteration., comment=Different type of impact, such as low-level amplification or whole gene deletion, should be recorded using the Reported impact Cluster within the CLUSTER.genetic_variant.v0 archetype., uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_CODED_TEXT, bindings=null, values=
  • Gain [A sequence alteration whereby the copy number of a given region is greater than the reference sequence.]
  • Loss [A sequence alteration whereby the copy number of a given region is less than the reference sequence.]
, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0004], code=at0004, itemType=SLOT, level=1, text=Reference sequence, description=The sequence file used as a reference to describe this variant., 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.v1 and specialisations, extendedValues=null]], minIndents={}, termBindingRetrievalErrorMessage=null]