ARCHETYPE Genomic conversion variant (openEHR-EHR-CLUSTER.genomic_conversion_variant.v1)

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

ARCHETYPE ID	openEHR-EHR-CLUSTER.genomic_conversion_variant.v1
Concept	Genomic conversion variant
Description	A human genetic sequence change where, compared to a genomic reference sequence, a range of nucleotides are replaced by a sequence from elsewhere in the genome.
Use	Use to record the details about a conversion 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.
Misuse	Not to be used to record information about variants of non-human DNA, or any kind of RNA or protein.
Purpose	To record the details about a conversion 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 - Conversion Variant [Internet]. Human Genome Variation Society. [2019] - [cited 2020-02-26]. Available from: https://varnomen.hgvs.org/recommendations/DNA/variant/conversion/
Copyright	© openEHR Foundation
Authors	Author name: Cecilia Mascia Organisation: CRS4, Italy Email: cecilia.mascia@crs4.it Date originally authored: 2017-02-24
Other Details Language	Author name: Cecilia Mascia Organisation: CRS4, Italy Email: cecilia.mascia@crs4.it Date originally authored: 2017-02-24
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 - Conversion Variant [Internet]. Human Genome Variation Society. [2019] - [cited 2020-02-26]. Available from: https://varnomen.hgvs.org/recommendations/DNA/variant/conversion/, original_namespace=org.openehr, original_publisher=openEHR Foundation, custodian_namespace=org.openehr, MD5-CAM-1.0.1=E8508DA94B907A913D6922DF808858BC, build_uid=521c792e-4323-45e2-84c5-d0f2fd4a5468, revision=1.0.3}
Keywords	conversion, variation, genetic, genomic, variant, DNA, chromosome, mutation, nucleotide
Lifecycle	published
UID	36eeb623-9630-4187-9150-d4b6398ef927
Language used	en
Citeable Identifier	1246.145.743
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 range of nucleotides are replaced by a sequence from elsewhere in the genome., archetypeConceptComment=null, otherContributors=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) Gideon Giacomelli, Charité Berlin, Germany 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, Natalia Strauch, University Hospital Heidelberg, Germany, Medizinische Hochschule Hannover, au.tomczak@yahoo.com, Strauch.Natalia@mh-hannover.de Norwegian Bokmål: Liv Laugen, OUS, 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[at0003], code=at0003, itemType=ELEMENT, level=1, text=Start converted position, description=The position of the first nucleotide of the converted range., comment=null, 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 converted position, description=The position of the last nucleotide of the converted range., comment=null, 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[at0009], code=at0009, itemType=ELEMENT, level=1, text=Replacing sequence start position, description=The position of the first nucleotide of the replacing sequence., comment=null, 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[at0010], code=at0010, itemType=ELEMENT, level=1, text=Replacing sequence end position, description=The position of the last nucleotide of the replacing sequence., comment=null, 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[at0011], code=at0011, itemType=SLOT, level=1, text=Converted reference sequence, description=The sequence file used as a reference to describe the converted region., 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], ResourceSimplifiedHierarchyItem [path=/items[at0012], code=at0012, itemType=SLOT, level=1, text=Replacing reference sequence, description=The sequence file used as a reference to describe the replacing region., 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=[], events=[], provider=[], identities=[], protocol=[]}, 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=2.., cardinalityText=Minimum of 2 items (Cardinality: 2.., ordered), subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=null, extendedValues=null]}, addHierarchyItemsTo=items, currentHierarchyItemsForAdding=[ResourceSimplifiedHierarchyItem [path=/items[at0003], code=at0003, itemType=ELEMENT, level=1, text=Start converted position, description=The position of the first nucleotide of the converted range., comment=null, 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 converted position, description=The position of the last nucleotide of the converted range., comment=null, 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[at0009], code=at0009, itemType=ELEMENT, level=1, text=Replacing sequence start position, description=The position of the first nucleotide of the replacing sequence., comment=null, 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[at0010], code=at0010, itemType=ELEMENT, level=1, text=Replacing sequence end position, description=The position of the last nucleotide of the replacing sequence., comment=null, 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[at0011], code=at0011, itemType=SLOT, level=1, text=Converted reference sequence, description=The sequence file used as a reference to describe the converted region., 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], ResourceSimplifiedHierarchyItem [path=/items[at0012], code=at0012, itemType=SLOT, level=1, text=Replacing reference sequence, description=The sequence file used as a reference to describe the replacing region., 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]