ARCHETYPE Genomic repeated sequence variant (openEHR-EHR-CLUSTER.genomic_repeated_sequence_variant.v1)

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

ARCHETYPE ID	openEHR-EHR-CLUSTER.genomic_repeated_sequence_variant.v1
Concept	Genomic repeated sequence variant
Description	A human genetic sequence change where, compared to a genomic reference sequence, a segment of one or more nucleotides (the repeat unit) is present several times, one after the other.
Use	Use to record the details about a repeated sequence 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 repeated sequence 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 - Repeated sequences Variant [Internet]. Human Genome Variation Society. [2019] - [cited 2020-02-26]. Available from: https://varnomen.hgvs.org/recommendations/DNA/variant/repeated/
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 - Repeated sequences Variant [Internet]. Human Genome Variation Society. [2019] - [cited 2020-02-26]. Available from: https://varnomen.hgvs.org/recommendations/DNA/variant/repeated/, original_namespace=org.openehr, original_publisher=openEHR Foundation, custodian_namespace=org.openehr, MD5-CAM-1.0.1=46FB5ED4B9ABE631DFE655742BFD3417, build_uid=86574d3b-6bc9-4020-a277-22059ac2d806, revision=1.0.3}
Keywords	repeated sequence, variation, genetic, genomic, variant, DNA, chromosome, mutation, nucleotide
Lifecycle	published
UID	f2b1d844-0ea6-4142-8d8e-181ea070d96e
Language used	en
Citeable Identifier	1013.1.3756
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 segment of one or more nucleotides (the repeat unit) is present several times, one after the other., archetypeConceptComment=For example: changing 'CACGGCCT' to 'CACGGcggcggCCT'., 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, Oslo University Hospital, Norway, liv.laugen@ous-hf.no , subjectOfData=unconstrained, archetypeTranslationTree=null, topLevelToAshis={source=[], identities=[], contacts=[], ism_transition=[], provider=[], protocol=[], description=[], events=[], details=[], context=[], target=[], capabilities=[], items=[ResourceSimplifiedHierarchyItem [path=/items[at0001], code=at0001, itemType=ELEMENT, level=1, text=Start position, description=Position of the first nucleotide of the repeated range., comment=For example: for a variant where the reference sequence 'CACGGCCT' is changed to 'CACGGcggcggCCT', 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 repeated range., comment=For example: for a variant where the reference sequence 'CACGGCCT' is changed to 'CACGGcggcggCCT', the end position is 5., 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[at0009], code=at0009, itemType=CLUSTER, level=1, text=Repeat unit, description=A repeated unit consisting of a repeated sequence and a copy number., comment=This cluster is repeatable to allow for mixed repeats. For example: for a variant where the reference sequence is 'GGC[9]GGA[1]GGC[10]', a mixed repeat could be 'GGC[10]GGA[1]GGC[9]GGA[1]GGC[10]'. The numbers in brackets in the example are the copy numbers., uncommonOntologyItems=null, occurencesFormal=1.., occurencesText=Mandatory, repeating, cardinalityFormal=1.., cardinalityText= (Cardinality: 1.., unordered), subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0009]/items[at0010], code=at0010, itemType=ELEMENT, level=2, text=Repeat order, description=The intended position of this repeat unit within the overall sequence of repeat units., comment=This element is only relevant for mixed repeats. For example: for a variant where the reference sequence is 'GGC[9]GGA[1]GGC[10]' and the mixed repeat is 'GGC[10]GGA[1]GGC[9]GGA[2]GGC[11]', the 'Repeat order' for 'GGC[10]' is 1, for 'GGA[1]' 2, for 'GGC[9]' 3, and so on., 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[at0009]/items[at0005], code=at0005, itemType=ELEMENT, level=2, text=Repeated sequence, description=The sequence of nucleotides that has been repeated., comment=For example: for a variant where the reference sequence 'CACGGCCT' is changed to 'CACGGcggcggCT', the repeated sequence is 'CGG'., 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]/items[at0007], code=at0007, itemType=ELEMENT, level=2, text=Copy number, description=The total number of times the 'Repeated sequence' was repeated., comment=For example: for a variant where the reference sequence 'CACGGCCT' is changed to 'CACGGcggcggCCT', the copy number is 3., uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_COUNT, bindings=null, values=min: >=2 , extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0008], code=at0008, 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]], other_participations=[], content=[], state=[], activities=[], data=[], relationships=[], credentials=[]}, 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[at0001], code=at0001, itemType=ELEMENT, level=1, text=Start position, description=Position of the first nucleotide of the repeated range., comment=For example: for a variant where the reference sequence 'CACGGCCT' is changed to 'CACGGcggcggCCT', 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 repeated range., comment=For example: for a variant where the reference sequence 'CACGGCCT' is changed to 'CACGGcggcggCCT', the end position is 5., 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[at0009], code=at0009, itemType=CLUSTER, level=1, text=Repeat unit, description=A repeated unit consisting of a repeated sequence and a copy number., comment=This cluster is repeatable to allow for mixed repeats. For example: for a variant where the reference sequence is 'GGC[9]GGA[1]GGC[10]', a mixed repeat could be 'GGC[10]GGA[1]GGC[9]GGA[1]GGC[10]'. The numbers in brackets in the example are the copy numbers., uncommonOntologyItems=null, occurencesFormal=1.., occurencesText=Mandatory, repeating, cardinalityFormal=1.., cardinalityText= (Cardinality: 1.., unordered), subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0009]/items[at0010], code=at0010, itemType=ELEMENT, level=2, text=Repeat order, description=The intended position of this repeat unit within the overall sequence of repeat units., comment=This element is only relevant for mixed repeats. For example: for a variant where the reference sequence is 'GGC[9]GGA[1]GGC[10]' and the mixed repeat is 'GGC[10]GGA[1]GGC[9]GGA[2]GGC[11]', the 'Repeat order' for 'GGC[10]' is 1, for 'GGA[1]' 2, for 'GGC[9]' 3, and so on., 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[at0009]/items[at0005], code=at0005, itemType=ELEMENT, level=2, text=Repeated sequence, description=The sequence of nucleotides that has been repeated., comment=For example: for a variant where the reference sequence 'CACGGCCT' is changed to 'CACGGcggcggCT', the repeated sequence is 'CGG'., 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]/items[at0007], code=at0007, itemType=ELEMENT, level=2, text=Copy number, description=The total number of times the 'Repeated sequence' was repeated., comment=For example: for a variant where the reference sequence 'CACGGCCT' is changed to 'CACGGcggcggCCT', the copy number is 3., uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_COUNT, bindings=null, values=min: >=2 , extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0008], code=at0008, 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]