ARCHETYPE Genomic duplication variant (openEHR-EHR-CLUSTER.genomic_duplication_variant.v1)

Name: Genomic duplication variant
License: http://creativecommons.org/licenses/by-sa/4.0/

ARCHETYPE ID	openEHR-EHR-CLUSTER.genomic_duplication_variant.v1
Concept	Genomic duplication variant
Description	A human genetic sequence change where, compared to a genomic reference sequence, a copy of one or more nucleotides are inserted directly 3' of the original copy of that sequence.
Use	Use to record the details about a duplication 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. In the examples in this archetype, lower case nucleotides are only intended to highlight the changed positions of the DNA sequence. All definitions and examples in this archetype follow the HGVS nomenclature.
Misuse	Not 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 when there is no evidence that the extra copy of a sequence detected is in tandem (directly 3’-flanking the original copy). Use the CLUSTER.genomic_insertion_variant archetype for this purpose.
Purpose	To record the details about a duplication variant of human DNA, observed in a genomic sequence.
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. Sequence Variant Nomenclature - DNA Recommendations - Duplication Variant [Internet]. Human Genome Variation Society. [2019] - [cited 2020-02-26]. Available from: https://varnomen.hgvs.org/recommendations/DNA/variant/duplication/
Copyright	© openEHR Foundation
Authors	Author name: Cecilia Mascia Organisation: CRS4, Italy Email: cecilia.mascia@crs4.it Date originally authored: 2017-02-23
Other Details Language	Author name: Cecilia Mascia Organisation: CRS4, Italy Email: cecilia.mascia@crs4.it Date originally authored: 2017-02-23
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. Sequence Variant Nomenclature - DNA Recommendations - Duplication Variant [Internet]. Human Genome Variation Society. [2019] - [cited 2020-02-26]. Available from: https://varnomen.hgvs.org/recommendations/DNA/variant/duplication/, original_namespace=org.openehr, original_publisher=openEHR Foundation, custodian_namespace=org.openehr, MD5-CAM-1.0.1=84C5AA6AA202ACEE0D0559072D8B207D, build_uid=36997faa-2f4f-4cab-9a24-f2a11ecc8381, revision=1.0.3}
Keywords	duplication, variation, genetic, genomic, variant, DNA, chromosome, mutation, nucleotide
Lifecycle	published
UID	c641090f-8ee6-4a93-a6fb-c201d53bcd79
Language used	en
Citeable Identifier	1246.145.740
Revision Number	1.0.3
All	Archetype [runtimeNameConstraintForConceptName=null, archetypeConceptBinding=null, archetypeConceptDescription=A human genetic sequence change where, compared to a genomic reference sequence, a copy of one or more nucleotides are inserted directly 3' of the original copy of that sequence., archetypeConceptComment=For example: changing 'AGtagaGG' to 'AGtagatagaGG'., otherContributors=Vebjørn Arntzen, Oslo University Hospital, Norway (openEHR Editor) Silje Ljosland Bakke, Helse Vest IKT AS, Norway (openEHR Editor) Francesca Frexia, CRS4, Italy Gideon Giacomelli, Charité Berlin, Germany Sjur Gjerald, Oslo University Hospital, Norway Christina Jaeger-Schmidt, Heidelberg University Hospital, Germany Florian Kaercher, Charité Berlin, Germany Liv Laugen, Oslo University Hospital, Norway, Norway Heather Leslie, Atomica Informatics, Australia (openEHR Editor) Cecilia Mascia, CRS4, Italy (openEHR Editor) Ian McNicoll, freshEHR Clinical Informatics, United Kingdom (openEHR Editor) Andrej Orel, Marand d.o.o., Slovenia Simon Schumacher, HiGHmed, Germany Aurelie Tomczak, Uniklinikum Heidelberg, Germany (openEHR Editor) Paolo Uva, CRS4, Italy Gianluigi Zanetti, CRS4, Italy 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, 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, Oslo University Hospital, Norway, liv.laugen@ous-hf.no , subjectOfData=unconstrained, archetypeTranslationTree=null, topLevelToAshis={relationships=[], source=[], capabilities=[], activities=[], details=[], context=[], ism_transition=[], other_participations=[], data=[], credentials=[], target=[], items=[ResourceSimplifiedHierarchyItem [path=/items[at0001], code=at0001, itemType=ELEMENT, level=1, text=Start position, description=Position of the duplicated nucleotide or the first nucleotide of the duplicated range., comment=For example: for a variant where the reference sequence 'AGtagaGG' is changed to 'AGtagatagaGG', the start position is 3., uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, 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=End position, description=Position of the last nucleotide of the duplicated range., comment=For example: for a variant where the reference sequence 'AGtagaGG' is changed to 'AGtagatagaGG', the end position is 6., 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=Duplicated sequence, description=The duplicated nucleotide or sequence., comment=For example: for a variant where the reference sequence 'AGtagaGG' is changed to 'AGtagatagaGG', the duplicated sequence is 'TAGA'., 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], code=at0006, itemType=SLOT, level=1, text=Reference sequence, description=The sequence file used as a reference to describe this variant., comment=null, 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]], content=[], description=[], contacts=[], 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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=End position, description=Position of the last nucleotide of the duplicated range., comment=For example: for a variant where the reference sequence 'AGtagaGG' is changed to 'AGtagatagaGG', the end position is 6., 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=Duplicated sequence, description=The duplicated nucleotide or sequence., comment=For example: for a variant where the reference sequence 'AGtagaGG' is changed to 'AGtagatagaGG', the duplicated sequence is 'TAGA'., 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], code=at0006, itemType=SLOT, level=1, text=Reference sequence, description=The sequence file used as a reference to describe this variant., comment=null, 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]