ARCHETYPE Genomic repeated sequence variant (openEHR-EHR-CLUSTER.genomic_repeated_sequence_variant.v0)

ARCHETYPE IDopenEHR-EHR-CLUSTER.genomic_repeated_sequence_variant.v0
ConceptGenomic repeated sequence variant
DescriptionA 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. For example: changing 'CACGGCCT' to 'CACGGcggcggCCT'.
UseUse 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.genetic_variant 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.
PurposeTo record the details about a repeated sequence variant of human DNA, observed in a genomic sequence.
Referencesden 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
AuthorsAuthor name: Cecilia Mascia
Organisation: CRS4, Italy
Email: cecilia.mascia@crs4.it
Date originally authored: 2017-02-24
Other Details LanguageAuthor 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=90B33D3C6BE5211B95D02E4E1EE66AA1, build_uid=da8ca0df-f7c1-46c3-a534-51b1095bca26, revision=0.0.1-alpha}
Keywordsrepeated sequence, variation, genetic, genomic, variant
Lifecyclein_development
UID1e33441a-f46d-4b93-99ab-34016267d90f
Language useden
Citeable Identifier1246.145.737
Revision Number0.0.1-alpha
AllArchetype [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. For example: changing 'CACGGCCT' to 'CACGGcggcggCCT'., archetypeConceptComment=For example: changing 'CGG' to 'CGGCGGCGG'., 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, Institute of Pathology, University Hospital Heidelberg, Germany, au.tomczak@yahoo.com
Norwegian Bokmål: Liv Laugen, Oslo University Hospital, Norway, ​Oslo University Hospital, Norway, liv.laugen@ous-hf.no
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, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0008], code=at0008, itemType=SLOT, level=1, text=Reference sequence, description=The sequence file that has been used as a reference to describe the 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]], protocol=[], relationships=[]}, 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, 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, in relation to the reference sequence., 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, in relation to the reference sequence., 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=, 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 that has been used as a reference to describe the 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]