ARCHETYPE Simple genetic variant (openEHR-EHR-CLUSTER.simple_variant.v0)

ARCHETYPE IDopenEHR-EHR-CLUSTER.simple_variant.v0
ConceptSimple genetic variant
DescriptionA sequence change where, compared to a reference sequence, a one or more nucleotides are changed.
UseThis archetype should be used inside the "Variant" SLOT of the "Genetic variant" archetype.
MisuseThis archetype should only be used for import of vcf-data if no annotation of the variant type (substitution, insertion etc.) is available, and, therefore, the right specific archetypes cannot be picked to store the variant results.
PurposeTo describe a variant observed in a sequence, where the variant type is unknown, for example, because no annotation of the data has yet been made, or because the specific variant is not covered by the specialized variant archetypes.
References"Den Dunnen et al. (2016) HGVS recommendations for the description of sequence variants: 2016 update. Hum.Mutat. 25: 37: 564-569"
Copyright© openEHR Foundation
AuthorsAuthor name: Aurelie Tomczak
Organisation: Institute of Pathology, University Hospital Heidelberg, Germany
Email: au.tomczak@yahoo.com
Date originally authored: 2020-06-18
Other Details LanguageAuthor name: Aurelie Tomczak
Organisation: Institute of Pathology, University Hospital Heidelberg, Germany
Email: au.tomczak@yahoo.com
Date originally authored: 2020-06-18
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 et al. (2016) HGVS recommendations for the description of sequence variants: 2016 update. Hum.Mutat. 25: 37: 564-569", original_namespace=org.openehr, original_publisher=openEHR Foundation, custodian_namespace=org.openehr, MD5-CAM-1.0.1=09EA89B3CD9789FFA9C8D61504F9620D, build_uid=413e04d6-5e97-4671-9155-4cb8f9877c58, revision=0.0.1-alpha}
Keywordsvariation, genetic, genomic, variant, simple generic variant
Lifecyclein_development
UID6330df99-9e38-4ab5-bce8-acd76b51ca5f
Language useden
Citeable Identifier1246.145.1296
Revision Number0.0.1-alpha
AllArchetype [runtimeNameConstraintForConceptName=null, archetypeConceptBinding=null, archetypeConceptDescription=A sequence change where, compared to a reference sequence, a one or more nucleotides are changed., 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, originalLanguage=en, translators=German: Aurelie Tomczak, Institute of Pathology, University Hospital Heidelberg, Germany, au.tomczak@yahoo.com
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  •  Coded Text
    • Chromosome 1 [Chromosome 1.]
    • Chromosome 2 [Chromosome 2.]
    • Chromosome 3 [Chromosome 3.]
    • Chromosome 4 [Chromosome 4.]
    • Chromosome 5 [Chromosome 5.]
    • Chromosome 6 [Chromosome 6.]
    • Chromosome 7 [Chromosome 7.]
    • Chromosome 8 [Chromosome 8.]
    • Chromosome 9 [Chromosome 9.]
    • Chromosome 10 [Chromosome 10.]
    • Chromosome 11 [Chromosome 11.]
    • Chromosome 12 [Chromosome 12.]
    • Chromosome 13 [Chromosome 13.]
    • Chromosome 14 [Chromosome 14.]
    • Chromosome 15 [Chromosome 15.]
    • Chromosome 16 [Chromosome 16.]
    • Chromosome 17 [Chromosome 17.]
    • Chromosome 18 [Chromosome 18.]
    • Chromosome 19 [Chromosome 19.]
    • Chromosome 20 [Chromosome 20.]
    • Chromosome 21 [Chromosome 21.]
    • Chromosome 22 [Chromosome 22.]
    • Chromosome X [Chromosome X.]
    • Chromosome Y [Chromosome Y.]
  •  Text
, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0003], code=at0003, itemType=ELEMENT, level=1, text=Start position of variant, description=The position of the first nucleotide of the changed range for a simple variant. ("Start" in vcf-file)., 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 position of variant, description=The position of the last nucleotide of the changed range for a simple variant. ("End" in vcf-file)., 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=Alternate nucleotide sequence, description=The observed alternate nucleotide or nucleotide sequence ("Alt" in vcf-file)., comment=null, uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0010], code=at0010, itemType=ELEMENT, level=1, text=Reference nucleotide sequence, description=The reference nucleotide or nucleotide sequence. ("Ref" in vcf-file)., comment=null, uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0038], code=at0038, 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:
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  •  Coded Text
    • Chromosome 1 [Chromosome 1.]
    • Chromosome 2 [Chromosome 2.]
    • Chromosome 3 [Chromosome 3.]
    • Chromosome 4 [Chromosome 4.]
    • Chromosome 5 [Chromosome 5.]
    • Chromosome 6 [Chromosome 6.]
    • Chromosome 7 [Chromosome 7.]
    • Chromosome 8 [Chromosome 8.]
    • Chromosome 9 [Chromosome 9.]
    • Chromosome 10 [Chromosome 10.]
    • Chromosome 11 [Chromosome 11.]
    • Chromosome 12 [Chromosome 12.]
    • Chromosome 13 [Chromosome 13.]
    • Chromosome 14 [Chromosome 14.]
    • Chromosome 15 [Chromosome 15.]
    • Chromosome 16 [Chromosome 16.]
    • Chromosome 17 [Chromosome 17.]
    • Chromosome 18 [Chromosome 18.]
    • Chromosome 19 [Chromosome 19.]
    • Chromosome 20 [Chromosome 20.]
    • Chromosome 21 [Chromosome 21.]
    • Chromosome 22 [Chromosome 22.]
    • Chromosome X [Chromosome X.]
    • Chromosome Y [Chromosome Y.]
  •  Text
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