ARCHETYPE Genomic inversion variant (openEHR-EHR-CLUSTER.genomic_inversion_variant.v1)

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

ARCHETYPE ID	openEHR-EHR-CLUSTER.genomic_inversion_variant.v1
Concept	Genomic inversion variant
Description	A human genetic sequence change where more than one nucleotide replaces the original sequence with the reverse complement of the original sequence, compared to a genomic reference sequence.
Use	Use to record the details about an inversion 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 one nucleotide inversion. Use the CLUSTER.genomic_substitution_variant archetype for this purpose.
Purpose	To record the details about an inversion 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 - Inversion Variant [Internet]. Human Genome Variation Society. [2019] - [cited 2020-02-26]. Available from: https://varnomen.hgvs.org/recommendations/DNA/variant/inversion/
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 - Inversion Variant [Internet]. Human Genome Variation Society. [2019] - [cited 2020-02-26]. Available from: https://varnomen.hgvs.org/recommendations/DNA/variant/inversion/, original_namespace=org.openehr, original_publisher=openEHR Foundation, custodian_namespace=org.openehr, MD5-CAM-1.0.1=8123D90C4AE8226BD888C84073372E1F, build_uid=a8b87105-6a60-410a-9d6d-09f644b3a011, revision=1.0.4}
Keywords	inversion, variation, genetic, genomic, variant, DNA, chromosome, mutation, nucleotide
Lifecycle	published
UID	e42a286f-b603-4b1d-8ba1-24e133abc18f
Language used	en
Citeable Identifier	1246.145.1345
Revision Number	1.0.4
All	Archetype [runtimeNameConstraintForConceptName=null, archetypeConceptBinding=null, archetypeConceptDescription=A human genetic sequence change where more than one nucleotide replaces the original sequence with the reverse complement of the original sequence, compared to a genomic reference sequence., archetypeConceptComment=For example: changing 'TCAG' to 'CTGA'., 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 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 Gyri Aasland Gradek, Haukeland University Hospital, Norway Asbjørg Stray-Pedersen, Oslo University Hospital, Norway Toril Fagerheim, University Hospital of Northern Norway, Norway Camilla F. Skjelbred, Telemark Hospital HF, 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, Silje Ljosland Bakke, Oslo University Hospital, Norway, Helse Vest IKT AS, Norway, liv.laugen@ous-hf.no, silje.ljosland.bakke@helse-vest-ikt.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 first nucleotide of the inverted range., comment=For example: for a variant where the reference sequence 'CAtcagCCT' is changed to 'CActgaCCT', 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[at0004], code=at0004, itemType=ELEMENT, level=1, text=End position, description=Position of the last nucleotide of the inverted range., comment=For example: for a variant where the reference sequence 'CAtcagCCT' is changed to 'CActgaCCT', the end position is 6., 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[at0006], code=at0006, itemType=ELEMENT, level=1, text=Inverted sequence, description=The inverted sequence., comment=For example: for a variant where the reference sequence 'CAtcagCCT' is changed to 'CActgaCCT', the inverted sequence is 'TCAG'., 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[at0007], code=at0007, 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=[], state=[], 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subCardinalityFormal=null, subCardinalityText=null, dataType=DV_COUNT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0004], code=at0004, itemType=ELEMENT, level=1, text=End position, description=Position of the last nucleotide of the inverted range., comment=For example: for a variant where the reference sequence 'CAtcagCCT' is changed to 'CActgaCCT', the end position is 6., 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[at0006], code=at0006, itemType=ELEMENT, level=1, text=Inverted sequence, description=The inverted sequence., comment=For example: for a variant where the reference sequence 'CAtcagCCT' is changed to 'CActgaCCT', the inverted sequence is 'TCAG'., 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[at0007], code=at0007, 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]