ARCHETYPE ID | openEHR-EHR-CLUSTER.inversion_variant.v1 |
Concept | Genetic variant - Inversion |
Description | A genetic sequence change where, compared to a reference sequence, more than one nucleotide replacing the original sequence are the reverse complement of the original sequence. |
Use | Use to record the details about an inversion variant of DNA or RNA, observed in a genetic sequence according to the HGVS nomenclature. This archetype has been specifically designed to be used in the 'Variant' SLOT within the CLUSTER.genetic_variant archetype, but can also be used within other ENTRY or CLUSTER archetypes, where clinically appropriate. |
Misuse | Not to be used to record a one nucleotide inversion. Use the CLUSTER.substitution_variant archetype for this purpose. |
Purpose | To record the details about an inversion variant of DNA or RNA, observed in a genetic sequence according to the HGVS nomenclature. |
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 - Inversion Variant [Internet]. Human Genome Variation Society. [2019] - [cited 2020-02-26]. Available from: https://varnomen.hgvs.org/recommendations/DNA/variant/inversion/ Sequence Variant Nomenclature - RNA Recommendations - Inversion Variant [Internet]. Human Genome Variation Society. [2019] - [cited 2020-03-04]. Available from: https://varnomen.hgvs.org/recommendations/RNA/variant/inversion/ |
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 - Inversion Variant [Internet]. Human Genome Variation Society. [2019] - [cited 2020-02-26]. Available from: https://varnomen.hgvs.org/recommendations/DNA/variant/inversion/ Sequence Variant Nomenclature - RNA Recommendations - Inversion Variant [Internet]. Human Genome Variation Society. [2019] - [cited 2020-03-04]. Available from: https://varnomen.hgvs.org/recommendations/RNA/variant/inversion/, original_namespace=org.openehr, original_publisher=openEHR Foundation, custodian_namespace=org.openehr, MD5-CAM-1.0.1=C63DF167330D3A78F14B61A3B16C6FF2, build_uid=a80a21c8-3675-4811-9baf-e36c14ba9abd, revision=1.0.1-alpha} |
Keywords | inversion, variation, genetic, genomic, variant |
Lifecycle | in_development |
UID | ee9f2fe2-e652-4324-a289-07eb3b720b89 |
Language used | en |
Citeable Identifier | 1013.1.4422 |
Revision Number | 1.0.1-alpha |
All | Archetype [runtimeNameConstraintForConceptName=null, archetypeConceptBinding=null, archetypeConceptDescription=A genetic sequence change where, compared to a reference sequence, more than one nucleotide replacing the original sequence are the reverse complement of the original sequence., archetypeConceptComment=For example: changing 'TCAG' to 'CTGA'., 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=
, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0004], code=at0004, itemType=ELEMENT, level=1, text=End position, description=Position of the last nucleotide of the inverted range, in relation to the reference sequence., comment=For example: for a genomic sequence variant where the reference sequence 'CAtcagCCT' is changed to 'CActgaCCT', the end position is 'g.6'., uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_PARSABLE, bindings=null, values=Formalism: HGVS-Variant-nomenclature , extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0006], code=at0006, itemType=ELEMENT, level=1, text=Inverted sequence, description=The nucleotide sequence of the reference sequence at the given positions., comment=For example: for a variant where the reference sequence 'CAtcagCCT' is changed to 'CActgaCCT', the inverted sequence is 'TCAG'., 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[at0007], code=at0007, 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_ , extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0004], code=at0004, itemType=ELEMENT, level=1, text=End position, description=Position of the last nucleotide of the inverted range, in relation to the reference sequence., comment=For example: for a genomic sequence variant where the reference sequence 'CAtcagCCT' is changed to 'CActgaCCT', the end position is 'g.6'., uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_PARSABLE, bindings=null, values=Formalism: HGVS-Variant-nomenclature , extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0006], code=at0006, itemType=ELEMENT, level=1, text=Inverted sequence, description=The nucleotide sequence of the reference sequence at the given positions., comment=For example: for a variant where the reference sequence 'CAtcagCCT' is changed to 'CActgaCCT', the inverted sequence is 'TCAG'., 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[at0007], code=at0007, 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_ |