ARCHETYPE Genomic copy number variant (openEHR-EHR-CLUSTER.genomic_copy_number_variant.v1)

ARCHETYPE IDopenEHR-EHR-CLUSTER.genomic_copy_number_variant.v1
ConceptGenomic copy number variant
DescriptionA human genetic sequence change where, compared to a genomic reference sequence, a DNA segment, usually larger than 1 kilobase (kb), 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.genomic_variant_result archetype, but can also be used within other ENTRY or CLUSTER archetypes, where clinically appropriate. All definitions and examples in this archetype follow the HGVS nomenclature.
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 information about tandem repeats. Use the CLUSTER.genomic_repeated_sequence_variant archetype for this purpose.
PurposeTo record the details about a copy number variant of human DNA, observed in a genomic sequence.
Referencesden Dunnen JT, Dalgleish R, Maglott DR, Hart RK, Greenblatt MS, McGowan-Jordan J, Roux AF, Smith T, Antonarakis SE, Taschner PE. HGVS Recommendations for the Description of Sequence Variants: 2016 Update. Hum Mutat. 2016 Jun;37(6):564-9. doi: 10.1002/humu.22981. Epub 2016 Mar 25. PubMed PMID: 26931183.
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, references=den Dunnen JT, Dalgleish R, Maglott DR, Hart RK, Greenblatt MS, McGowan-Jordan J, Roux AF, Smith T, Antonarakis SE, Taschner PE. HGVS Recommendations for the Description of Sequence Variants: 2016 Update. Hum Mutat. 2016 Jun;37(6):564-9. doi: 10.1002/humu.22981. Epub 2016 Mar 25. PubMed PMID: 26931183., original_namespace=org.openehr, original_publisher=openEHR Foundation, custodian_namespace=org.openehr, MD5-CAM-1.0.1=811AEF4A98143C4B70BA9CD97316F80F, build_uid=aa20f6e1-9456-4bfc-b836-f3ef4238e780, revision=1.1.0}
Keywordscopy number, variation, genetic, genomic, variant, DNA, chromosome, mutation, nucleotide
Lifecyclepublished
UID69e173a1-6963-4313-a500-669da9fc11b4
Language useden
Citeable Identifier1013.1.3750
Revision Number1.1.0
AllArchetype [runtimeNameConstraintForConceptName=null, archetypeConceptBinding=null, archetypeConceptDescription=A human genetic sequence change where, compared to a genomic reference sequence, a DNA segment, usually larger than 1 kilobase (kb), was deleted or duplicated., archetypeConceptComment=null, otherContributors=Gyri Aasland Gradek, Haukeland University Hospital, Norway
Vebjørn Arntzen, Oslo University Hospital, Norway (openEHR Editor)
Silje Ljosland Bakke, Helse Vest IKT AS, Norway (openEHR Editor)
Dag Erik Undlien, Oslo University Hospital, Norway
Camilla F. Skjelbred, Telemark HF Hospital, Norway
Toril Fagerheim, University Hospital of North Norway, Norway
Francesca Frexia, CRS4, Italy
Sjur Gjerald, Oslo University Hospital, Norway
Gunnar Houge, Haukeland University Hospital, Norway
Christina Jaeger-Schmidt, Heidelberg University Hospital, Germany
Florian Kaercher, Charité Berlin, Germany
Liv Laugen, ​Oslo University Hospital, Norway, Norway (openEHR Editor)
Heather Leslie, Atomica Informatics, Australia (openEHR Editor)
Cecilia Mascia, CRS4, Italy (openEHR Editor)
Simon Schumacher, HiGHmed, Germany
Asbjørg Stray-Pedersen, Oslo University Hospital, Norway
Nyree Taylor, Ocean Health Systems, Australia
Aurelie Tomczak, Uniklinikum Heidelberg, Germany
Paolo Uva, CRS4, Italy
Gianluigi Zanetti, CRS4, Italy
Rune Østern, St Olavs Hospital, Norway, originalLanguage=en, translators=
  • German: Aurelie Tomczak, Natalia Strauch, Institute of Pathology, University Hospital Heidelberg, Germany; Medizinische Hochschule Hannover, au.tomczak@yahoo.com, Strauch.Natalia@mh-hannover.de
  • Norwegian Bokmål: Liv Laugen, ​Oslo University Hospital, Norway, liv.laugen@ous-hf.no
, subjectOfData=unconstrained, archetypeTranslationTree=null, topLevelToAshis={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=CHOICE, bindings=null, values=Choice of:
  •  Count
    min: >=0

  •  Quantity
    Property: Qualified real
, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0005], code=at0005, itemType=ELEMENT, level=1, text=Copy number change type, description=Type of sequence alteration., comment=Different types of impact, such as low-level amplification or whole gene deletion, should be recorded using the 'Functional impact' Cluster within the CLUSTER.genomic_variant_result 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]], description=[], context=[], activities=[], identities=[], capabilities=[], provider=[], protocol=[], content=[], source=[], credentials=[], events=[], data=[], contacts=[], ism_transition=[], details=[], relationships=[], state=[], target=[], other_participations=[]}, 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=CHOICE, bindings=null, values=Choice of:
  •  Count
    min: >=0

  •  Quantity
    Property: Qualified real
, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0005], code=at0005, itemType=ELEMENT, level=1, text=Copy number change type, description=Type of sequence alteration., comment=Different types of impact, such as low-level amplification or whole gene deletion, should be recorded using the 'Functional impact' Cluster within the CLUSTER.genomic_variant_result 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]