ARCHETYPE Genomic deletion variant (openEHR-EHR-CLUSTER.genomic_deletion_variant.v1)

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

ARCHETYPE ID	openEHR-EHR-CLUSTER.genomic_deletion_variant.v1
Concept	Genomic deletion variant
Description	A human genetic sequence change where, compared to a genomic reference sequence, one or more nucleotides are not present (deleted).
Use	Use to record the details about a deletion 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.
Purpose	To record the details about a deletion 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 - Deletion Variant [Internet]. Human Genome Variation Society. [2019] - [cited 2020-02-26]. Available from: https://varnomen.hgvs.org/recommendations/DNA/variant/deletion/
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 - Deletion Variant [Internet]. Human Genome Variation Society. [2019] - [cited 2020-02-26]. Available from: https://varnomen.hgvs.org/recommendations/DNA/variant/deletion/, original_namespace=org.openehr, original_publisher=openEHR Foundation, custodian_namespace=org.openehr, MD5-CAM-1.0.1=4FB63ECCC6FB04AA640F8B2F731487A4, build_uid=9e865cfb-29dc-4b7f-a816-be2c9c225026, revision=1.0.3}
Keywords	deletion, variation, genetic, genomic, variant, DNA, chromosome, mutation, nucleotide
Lifecycle	published
UID	d8b03cd4-44ab-4ecc-afb4-fd18512e6b65
Language used	en
Citeable Identifier	1246.145.739
Revision Number	1.0.3
All	Archetype [runtimeNameConstraintForConceptName=null, archetypeConceptBinding=null, archetypeConceptDescription=A human genetic sequence change where, compared to a genomic reference sequence, one or more nucleotides are not present (deleted)., archetypeConceptComment=For example: changing 'AGAAtCACA' to 'AGAA_CACA'., otherContributors=Vebjørn Arntzen, Oslo University Hospital, Norway (openEHR Editor) Silje Ljosland Bakke, Helse Vest IKT AS, Norway (openEHR Editor) SB Bhattacharyya, Sudisa Consultancy Services, India Francesca Frexia, CRS4 - Center for advanced studies, research and development in Sardinia, Italy Gideon Giacomelli, Charité Berlin, Germany Heather Grain, Llewelyn Grain Informatics, Australia Evelyn Hovenga, EJSH Consulting, Australia Christina Jaeger-Schmidt, Heidelberg University Hospital, Germany Florian Kaercher, Charité Berlin, Germany 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 Natalia Strauch, Medizinische Hochschule Hannover, Germany Aurelie Tomczak, Uniklinikum Heidelberg, Germany Paolo Uva, CRS4, Italy Gianluigi Zanetti, CRS4, Italy, 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={state=[], content=[], source=[], events=[], capabilities=[], details=[], protocol=[], provider=[], data=[], activities=[], contacts=[], identities=[], relationships=[], description=[], ism_transition=[], target=[], credentials=[], items=[ResourceSimplifiedHierarchyItem [path=/items[at0001], code=at0001, itemType=ELEMENT, level=1, text=Start position, description=Position of the deleted nucleotide or the first nucleotide of the deleted range., comment=For example: for a variant where the reference sequence 'AGAatcACA' is changed to 'AGA___ACA' the start position is 4., 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[at0005], code=at0005, itemType=ELEMENT, level=1, text=End position, description=Position of the last nucleotide of the deleted range., comment=For example: for a variant where the reference sequence 'AGAatcACA' is changed to 'AGA___ACA' 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[at0008], code=at0008, itemType=ELEMENT, level=1, text=Deleted sequence, description=The deleted nucleotide or sequence., comment=For example: for a variant where the reference sequence 'AGAatcACA' is changed to 'AGA___ACA' the deleted sequence is 'ATC'., 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[at0009], code=at0009, 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]], context=[], 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= (Cardinality: 1.., unordered), 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 position, description=Position of the deleted nucleotide or the first nucleotide of the deleted range., comment=For example: for a variant where the reference sequence 'AGAatcACA' is changed to 'AGA___ACA' the start position is 4., 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[at0005], code=at0005, itemType=ELEMENT, level=1, text=End position, description=Position of the last nucleotide of the deleted range., comment=For example: for a variant where the reference sequence 'AGAatcACA' is changed to 'AGA___ACA' 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[at0008], code=at0008, itemType=ELEMENT, level=1, text=Deleted sequence, description=The deleted nucleotide or sequence., comment=For example: for a variant where the reference sequence 'AGAatcACA' is changed to 'AGA___ACA' the deleted sequence is 'ATC'., 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[at0009], code=at0009, 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]