ARCHETYPE Genomic variant result (openEHR-EHR-CLUSTER.genetic_variant.v0)

ARCHETYPE IDopenEHR-EHR-CLUSTER.genetic_variant.v0
ConceptGenomic variant result
DescriptionResult of a genomic test for a single variant in a human individual.
UseUse to report findings and annotations related to a single mutation found in the genome by a sequencing test. This archetype is meant to be used in the "Test result" SLOT of the Laboratory test result observation archetype. Use to report findings and annotations related to a single mutation found in the genome by a sequencing test. At implementation, the decision about which variant data should be stored in different applications, such as clinical EHRs or research databases, needs to be done on a case by case basis. This archetype allows the recording of genomic variants in both the HGVS syntax in an inline parsable element, and an atomic, structured form through the use of a nested CLUSTER archetype for specific variant types. If both of those representations are used simultaneously, they need to represent identical data.
MisuseNot to be used for recording information about the comparison of several samples. Use a specific archetype for this purpose.
PurposeTo report findings and annotations related to a single mutation found in the genome by a sequencing test.
ReferencesDerived from: <Add reference to original resource here>
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 variants available from: https://varnomen.hgvs.org/.

HL7 FHIR R4 [Internet]. HL7 International; 2018. Genomic Implementation Guidance; 2018 [cited 2019 05 23]. Available from: https://www.hl7.org/fhir/genomics.html.

Rehm HL, Bale SJ, Bayrak-Toydemir P, Berg JS, Brown KK, Deignan JL, Friez MJ, Funke BH, Hegde MR, Lyon E. ACMG clinical laboratory standards for next-generation sequencing. Genet Med. 2013 Sep;15(9):733-47. doi: 10.1038/gim.2013.92. Epub 2013 Jul 25. PubMed PMID: 23887774; PubMed Central PMCID: PMC4098820.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5. PubMed PMID: 25741868; PubMed Central PMCID: PMC4544753.
Copyright© openEHR Foundation, HiGHmed
AuthorsAuthor name: Cecilia Mascia
Organisation: CRS4, Italy
Email: cecilia.mascia@crs4.it
Date originally authored: 2019-01-15
Other Details LanguageAuthor name: Cecilia Mascia
Organisation: CRS4, Italy
Email: cecilia.mascia@crs4.it
Date originally authored: 2019-01-15
OtherDetails Language Independent{licence=This work is licensed under the Creative Commons Attribution-ShareAlike 3.0 License. To view a copy of this license, visit http://creativecommons.org/licenses/by-sa/3.0/., custodian_organisation=HiGHmed, references=Derived from: 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 variants available from: https://varnomen.hgvs.org/. HL7 FHIR R4 [Internet]. HL7 International; 2018. Genomic Implementation Guidance; 2018 [cited 2019 05 23]. Available from: https://www.hl7.org/fhir/genomics.html. Rehm HL, Bale SJ, Bayrak-Toydemir P, Berg JS, Brown KK, Deignan JL, Friez MJ, Funke BH, Hegde MR, Lyon E. ACMG clinical laboratory standards for next-generation sequencing. Genet Med. 2013 Sep;15(9):733-47. doi: 10.1038/gim.2013.92. Epub 2013 Jul 25. PubMed PMID: 23887774; PubMed Central PMCID: PMC4098820. Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5. PubMed PMID: 25741868; PubMed Central PMCID: PMC4544753., original_namespace=org.highmed, custodian_namespace=org.highmed, original_publisher=HiGHmed, MD5-CAM-1.0.1=1F87612FB91ED1282ED06A7B1C0B1838, build_uid=48a7eec9-3c11-4ffe-8419-2f4776935478, revision=0.0.1-alpha}
Keywordsvariation, VCF, variant, genetic, genomic, variant calling, sequence, mutation, allele, genotype
Lifecyclein_development
UID475cf4d3-4684-4d9c-9081-5d16788d8ad7
Language useden
Citeable Identifier1246.145.1374
Revision Number0.0.1-alpha
AllArchetype [runtimeNameConstraintForConceptName=null, archetypeConceptBinding=null, archetypeConceptDescription=Result of a genomic test for a single variant in a human individual., archetypeConceptComment=null, 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
Shahla Foozonkhah, Iran ministry of health and education, Iran
Francesca Frexia, CRS4 - Center for advanced studies, research and development in Sardinia, Italy
Gideon Giacomelli, Charité Berlin, Germany
Sjur Gjerald, Oslo University Hospital, Norway
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)
Shane McKee, Belfast Health & Social Care Trust, United Kingdom
Ian McNicoll, freshEHR Clinical Informatics, United Kingdom (openEHR Editor)
Andrej Orel, Marand d.o.o., Slovenia
Niklas Reimer, Institut für Medizinische Informatik / Universität zu Lübeck, Germany
Simon Schumacher, HiGHmed, Germany
Natalia Strauch, Medizinische Hochschule Hannover, Germany
Nyree Taylor, Ocean Informatics, Australia
Aurelie Tomczak, Uniklinikum Heidelberg, Germany (openEHR Editor)
Paolo Uva, CRS4, Italy
John Tore Valand, Helse Bergen, Norway
Gianluigi Zanetti, CRS4, Italy, originalLanguage=en, translators=German: Aurelie Tomczak, Institute of Pathology, University Hospital Heidelberg, au.tomczak@yahoo.com
Norwegian Bokmål: Vebjørn Arntzen / Liv Laugen, ​Oslo University Hospital, Norway, varntzen@ous-hf.no, liv.laugen@ous-hf.no
, subjectOfData=unconstrained, archetypeTranslationTree=null, topLevelToAshis={details=[], provider=[], activities=[], data=[], capabilities=[], description=[], contacts=[], credentials=[], events=[], other_participations=[], state=[], ism_transition=[], source=[], target=[], protocol=[], context=[], content=[], relationships=[], identities=[], items=[ResourceSimplifiedHierarchyItem [path=/items[at0001], code=at0001, itemType=SLOT, level=1, text=Bioinformatic analysis workflow, description=Structured details about the bioinformatic analysis workflow or a link to a protocol., comment=null, uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=Include:
openEHR-EHR-CLUSTER.knowledge_base.v0 and specialisations Or
openEHR-EHR-CLUSTER.knowledge_base.v1 and specialisations Or
openEHR-EHR-CLUSTER.device.v1 and specialisations, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0002], code=at0002, itemType=SLOT, level=1, text=Reference genome, description=Structured details about the specific version of the human sequence assembly used for annotation., comment=For example, "GCF_000001405.38" Source name: NCBI Accession number: GCF_000001405 Version number: GCF_000001405.38 URL: https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.38/, uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=Include:
openEHR-EHR-CLUSTER.reference_sequence.v1 and specialisations, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0003], code=at0003, itemType=CLUSTER, level=1, text=Variant identifier, description=A reference to a specific variation recorded into a biological variation database., comment=For example: rs123456 (Identification) from dbSNP (Source name) version 151 (version). This internal cluster is repeatable to allow several different IDs from different databases for the same variant., uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=1..*, cardinalityText=, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0003]/items[at0004], code=at0004, itemType=ELEMENT, level=2, text=Source name, description=The name of the public data source that gives the variant identification., 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[at0003]/items[at0005], code=at0005, itemType=ELEMENT, level=2, text=Identification, description=The ID of a variation record., 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[at0003]/items[at0006], code=at0006, itemType=ELEMENT, level=2, text=Version, description=The exact version of the record., comment=null, 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[at0003]/items[at0007], code=at0007, itemType=ELEMENT, level=2, text=URL, description=A reference to a specific variation recorded into a biological variation database., comment=null, uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_URI, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0101], code=at0101, itemType=ELEMENT, level=1, text=Variant, description=Description of the variation at the genomic level following the HGVS nomenclature., comment=For example: "g.33038255C>A". If both this element and the "Structured variant" SLOT are used simultaneously, they need to represent identical data., uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_PARSABLE, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0045], code=at0045, itemType=SLOT, level=1, text=Structured variant, description=Structured description of the genomic variant., comment=This element is set to multiple occurrence to allow templates to be built with several different variant types allowed. However, when storing data, there should never be more than one CLUSTER archetype inserted here. If both this SLOT and the "Variant" data element are used simultaneously, they need to represent identical data., uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=Include:
openEHR-EHR-CLUSTER.repeated_sequence_variant.v0 and specialisations Or
openEHR-EHR-CLUSTER.inversion_variant.v0 and specialisations Or
openEHR-EHR-CLUSTER.substitution_variant.v0 and specialisations Or
openEHR-EHR-CLUSTER.indel_variant.v0 and specialisations Or
openEHR-EHR-CLUSTER.duplication_variant.v0 and specialisations Or
openEHR-EHR-CLUSTER.deletion_variant.v0 and specialisations Or
openEHR-EHR-CLUSTER.conversion_variant.v0 and specialisations Or
openEHR-EHR-CLUSTER.insertion_variant.v0 and specialisations Or
openEHR-EHR-CLUSTER.copy_number_variant.v0 and specialisations Or
openEHR-EHR-CLUSTER.translocation_variant.v0 and specialisations Or
openEHR-EHR-CLUSTER.repeated_sequence_variant.v1 and specialisations Or
openEHR-EHR-CLUSTER.inversion_variant.v1 and specialisations Or
openEHR-EHR-CLUSTER.substitution_variant.v1 and specialisations Or
openEHR-EHR-CLUSTER.indel_variant.v1 and specialisations Or
openEHR-EHR-CLUSTER.duplication_variant.v1 and specialisations Or
openEHR-EHR-CLUSTER.deletion_variant.v1 and specialisations Or
openEHR-EHR-CLUSTER.conversion_variant.v1 and specialisations Or
openEHR-EHR-CLUSTER.insertion_variant.v1 and specialisations Or
openEHR-EHR-CLUSTER.copy_number_variant.v1 and specialisations Or
openEHR-EHR-CLUSTER.translocation_variant.v1 and specialisations, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0008], code=at0008, itemType=CLUSTER, level=1, text=Transcript, description=Structured details about the transcript which is potentially affected by the variant., comment=null, uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=1..*, cardinalityText=, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0008]/items[at0009], code=at0009, itemType=SLOT, level=2, text=Transcript reference sequence, description=Structured details about the transcribed reference sequence., comment=Example: Source name: NCBI Accession number: NM_015557 Version number: NM_015557.2 URL: https://www.ncbi.nlm.nih.gov/nuccore/304361774, uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=[LOINC(2.65)::51958-7 | Transcript reference sequence [ID]], values=Include:
openEHR-EHR-CLUSTER.reference_sequence.v1 and specialisations, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0008]/items[at0010], code=at0010, itemType=ELEMENT, level=2, text=DNA region name, description=A human readable name for the region of interest., comment=For example: Exon number, intron number, splice site or other., uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_TEXT, bindings=[LOINC(2.65)::47999-8 | DNA region name [Identifier]], values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0008]/items[at0099], code=at0099, itemType=ELEMENT, level=2, text=Distance from splicing site, description=Distance in nucleotides between mutation and exon–intron junction., comment=null, 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]/items[at0011], code=at0011, itemType=ELEMENT, level=2, text=DNA change, description=Description of the variation at the DNA level following the HGVS nomenclature., comment=For example: "c.5249C>T"., uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_PARSABLE, bindings=[LOINC(2.65)::48004-6 | DNA change (c.HGVS)], values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0008]/items[at0012], code=at0012, itemType=ELEMENT, level=2, text=Amino acid change, description=Description of the variation at the protein level following the HGVS nomenclature., comment=For example: "p.T1750M"., uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_PARSABLE, bindings=[LOINC(2.65)::48005-3 | Amino acid change (pHGVS)], values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0008]/items[at0013], code=at0013, itemType=ELEMENT, level=2, text=Amino acid change type, description=Codified type for associated Amino Acid Marker., comment=null, uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CHOICE, bindings=[LOINC(2.65)::48006-1 | Amino acid change [Type]], values=Choice of:
  •  Coded Text
    • Wild type [The sequence at a given position is identical to the reference sequence.]
      [LOINC(2.65)::LA9658-1]
    • Deletion [A deletion in the amino acid sequence.]
      [LOINC(2.65)::LA6692-3]
    • Duplication [A duplication in the amino acid sequence.]
      [LOINC(2.65)::LA6686-5]
    • Frameshift [A frameshift in the amino acid sequence.]
      [LOINC(2.65)::LA6694-9]
    • Initiating methionine [A variant in a sequence affecting the translation initiation codon.]
      [LOINC(2.65)::LA6695-6]
    • Insertion [A insertion in the amino acid sequence.]
      [LOINC(2.65)::LA6687-3]
    • Insertion and deletion [An insertion/deletion in the amino acid sequence.]
      [LOINC(2.65)::LA9659-9]
    • Missense [A variant in a protein sequence where, compared to the reference sequence, one amino acid is replaced by another amino acid.]
      [LOINC(2.65)::LA6698-0]
    • Nonsense [A variant in a protein sequence where, compared to the reference sequence, an amino acid is replaced by a translational stop codon (termination codon).]
      [LOINC(2.65)::LA6699-8]
    • Silent [A variant in a DNA sequence that does not change the amino acid sequence of the encoded protein.]
      [LOINC(2.65)::LA6700-4]
    • Stop codon mutation [A variant in a sequence affecting the translational stop codon.]
      [LOINC(2.65)::LA6701-2]
  •  Text
, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0008]/items[at0100], code=at0100, itemType=ELEMENT, level=2, text=RNA change, description=Description of the variation at the RNA level following the HGVS nomenclature., comment=For example: "r.76a>u"., uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_PARSABLE, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0008]/items[at0015], code=at0015, itemType=CLUSTER, level=2, text=Predicted impact, description=Estimate of the effects that the variant may have on the transcript., comment=Calculation is based on a precise data source and only done by software. For example: If we have a CADD score of 30 for pathogenicity prediction, we’ll record: - Predicted Impact Analysis: CADD - Score: 30 - Qualitative prediction: probably damaging., uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=1..*, cardinalityText=, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0008]/items[at0015]/items[at0016], code=at0016, itemType=SLOT, level=3, text=Predicted impact analysis, description=Structured details about the tool used to calculate the predicted impact., comment=For example "CADD", "SIFT", etc., uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=Include:
openEHR-EHR-CLUSTER.knowledge_base.v0 and specialisations Or
openEHR-EHR-CLUSTER.knowledge_base.v1 and specialisations Or
openEHR-EHR-CLUSTER.device.v1 and specialisations, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0008]/items[at0015]/items[at0017], code=at0017, itemType=ELEMENT, level=3, text=Score, description=The calculated value., comment=null, uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=C_DV_QUANTITY, bindings=null, values=Property: Qualified real
Units:
, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0008]/items[at0015]/items[at0018], code=at0018, itemType=ELEMENT, level=3, text=Qualitative prediction, description=Human readable version of the predicted impact., comment=null, 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[at0008]/items[at0052], code=at0052, itemType=CLUSTER, level=2, text=Reported impact, description=Intepretation of the Mutation linked to a specific paper., comment=For example: activation, deactivating, dysfunction., uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=1..*, cardinalityText=, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0008]/items[at0052]/items[at0053], code=at0053, itemType=SLOT, level=3, text=Source, description=A reference to the specific research paper., 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.citation.v0 and specialisations Or
openEHR-EHR-CLUSTER.citation.v1 and specialisations, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0008]/items[at0052]/items[at0054], code=at0054, itemType=ELEMENT, level=3, text=Impact, description=Interpretative data about the specific variant., 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[at0008]/items[at0019], code=at0019, itemType=CLUSTER, level=2, text=Gene, description=Structured details about the gene harboring the variant., comment=null, uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=1..*, cardinalityText=, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0008]/items[at0019]/items[at0020], code=at0020, itemType=ELEMENT, level=3, text=Gene symbol, description=The official gene symbol approved by the HGNC, which is a short abbreviated form of the gene name., comment=For example "CHD5"., 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[at0008]/items[at0019]/items[at0021], code=at0021, itemType=ELEMENT, level=3, text=Full name, description=The full gene name approved by the HGNC that convey the character or function of the gene., comment=For example "Chromodomain helicase DNA binding protein 5"., 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[at0008]/items[at0019]/items[at0056], code=at0056, itemType=ELEMENT, level=3, text=Copy number overlap, description=The fraction of gene region covered by copy number., comment=null, uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_PROPORTION, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0008]/items[at0019]/items[at0057], code=at0057, itemType=ELEMENT, level=3, text=Part of fusion, description=States if the Gene is part of a Fusion Gene and if it is the first or second part of the Fusion Gene., comment=null, uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_CODED_TEXT, bindings=null, values=
  • First [First part of a Fusion Gene.]
  • Second [Second part of a Fusion Gene.]
, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0008]/items[at0058], code=at0058, itemType=ELEMENT, level=2, text=ACMG classification, description=Single DNA marker or individual allele interpretation in the context of the assessed genetic disease according to the ACMG recommendations., comment=null, uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_CODED_TEXT, bindings=[LOINC(2.65)::53037-8 | Genetic variation clinical significance [Imp]], values=
  • Pathogenic [Pathogenic variant.]
    [LOINC(2.65)::LA6668-3]
  • Likely pathogenic [Likely pathogenic variant.]
    [LOINC(2.65)::LA26332-9]
  • Uncertain significance [Variant of uncertain significance.]
    [LOINC(2.65)::LA26333-7]
  • Likely benign [Likely benign variant.]
    [LOINC(2.65)::LA26334-5]
  • Benign [Benign variant.]
    [LOINC(2.65)::LA6675-8]
, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0008]/items[at0059], code=at0059, itemType=ELEMENT, level=2, text=Fusion exon, description=The number of the exon which is either the end or the beginning of the fusion., comment=null, 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[at0023], code=at0023, itemType=ELEMENT, level=1, text=Best transcript candidate, description=The ID of the transcript with the highest predicted impact., comment=null, 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[at0024], code=at0024, itemType=CLUSTER, level=1, text=Conservation, description=Structured details about the evolutionary conservation., comment=null, uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=1..*, cardinalityText=, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0024]/items[at0025], code=at0025, itemType=SLOT, level=2, text=Conservation score analysis, description=Structured details about the tool used to calculate the conservation score., comment=For example "PhastCons7-way"., uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=Include:
openEHR-EHR-CLUSTER.knowledge_base.v0 and specialisations Or
openEHR-EHR-CLUSTER.knowledge_base.v1 and specialisations Or
openEHR-EHR-CLUSTER.device.v1 and specialisations, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0024]/items[at0026], code=at0026, itemType=ELEMENT, level=2, text=Score, description=The conservation score., comment=null, uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=C_DV_QUANTITY, bindings=null, values=Property: Qualified real
Units:
, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0060], code=at0060, itemType=ELEMENT, level=1, text=Read depth, description=Total number of reads mapped at this specific location., comment=null, 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[at0028], code=at0028, itemType=ELEMENT, level=1, text=Allele depth, description=The number of reads that support the reported variant., comment=null, 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[at0047], code=at0047, itemType=ELEMENT, level=1, text=Allele frequency, description=The relative frequency of an allele at a particular locus, expressed as a number from 0 to 1., comment=null, uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=C_DV_QUANTITY, bindings=[LOINC(2.65)::81258-6 | Allelic frequency [NFr]], values=Property: Qualified real
Units:
  • 0.0..1.0
, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0029], code=at0029, itemType=CLUSTER, level=1, text=Population allele frequency details, description=The relative frequency of a particular allele in the population, expressed as a number from 0 to 1., comment=null, uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=1..*, cardinalityText=, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0029]/items[at0030], code=at0030, itemType=SLOT, level=2, text=Population allele frequency analysis, description=Structured details about the database used to calculate the allele frequency., comment=null, uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=Include:
openEHR-EHR-CLUSTER.knowledge_base.v0 and specialisations Or
openEHR-EHR-CLUSTER.knowledge_base.v1 and specialisations Or
openEHR-EHR-CLUSTER.device.v1 and specialisations, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0029]/items[at0031], code=at0031, itemType=ELEMENT, level=2, text=Population allele frequency, description=The population allele frequency., comment=null, uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=C_DV_QUANTITY, bindings=[LOINC(2.65)::81258-6 | Allelic frequency [NFr]], values=Property: Qualified real
Units:
  • 0.0..1.0
, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0061], code=at0061, itemType=CLUSTER, level=1, text=VCF quality filter, description=Structured details about the quality filters that have been applied to the data., comment=This field is derived from the FILTER column of VCF. , uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=1..*, cardinalityText=, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0061]/items[at0062], code=at0062, itemType=ELEMENT, level=2, text=Filter name, description=Name of the quality filter., comment=For example "q10"., 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[at0061]/items[at0063], code=at0063, itemType=ELEMENT, level=2, text=Description, description=Quality filter extended description., comment=For example "at this site the quality is below 10"., 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[at0061]/items[at0064], code=at0064, itemType=ELEMENT, level=2, text=Filter passed, description=Whether the variant passed the quality filter., comment=Record as True if the filter was passed., uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_BOOLEAN, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0067], code=at0067, itemType=ELEMENT, level=1, text=Strand bias ratio, description=The ratio of the strand bias., comment=null, uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=C_DV_QUANTITY, bindings=null, values=Property: Qualified real
Units:
, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0068], code=at0068, itemType=ELEMENT, level=1, text=Strand bias p-value, description=The Phred-scaled p-value of the strand bias., comment=null, uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=C_DV_QUANTITY, bindings=null, values=Property: Qualified real
Units:
, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0039], code=at0039, itemType=ELEMENT, level=1, text=Genotype, description=Genotype encoded as allele values separated by either of / or | (0 for the reference allele, 1 for the first alternate, etc.)., 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[at0040], code=at0040, itemType=ELEMENT, level=1, text=Allelic state, description=The level of occurrence of a single DNA Marker within a set of chromosomes., comment=This is the human readable version of genotype, e.g.: Heterozygous, Homozygous., uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CHOICE, bindings=[LOINC(2.65)::53034-5 | Allelic state], values=Choice of:
  •  Coded Text
    • Heteroplasmic [Heteroplasmic.]
      [LOINC(2.65)::LA6703-8]
    • Homoplasmic [Homoplasmic.]
      [LOINC(2.65)::LA6704-6]
    • Homozygous [Homozygous.]
      [LOINC(2.65)::LA6705-3]
    • Heterozygous [Heterozygous.]
      [LOINC(2.65)::LA6706-1]
    • Hemizygous [Hemizygous.]
      [LOINC(2.65)::LA6707-9]
  •  Text
, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0041], code=at0041, itemType=ELEMENT, level=1, text=Genotype quality, description=Conditional genotype quality, encoded as a phred quality., comment=null, uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_COUNT, bindings=null, values=min: >=0

, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0069], code=at0069, itemType=ELEMENT, level=1, text=Genotype probability, description=A comma separated list of the log10-scaled genotype likelihoods for all possible genotypes, given the reference and the alternate alleles., comment=null, 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[at0070], code=at0070, itemType=ELEMENT, level=1, text=Specimen identifier, description=Identification of the specimen used for the genomic result., comment=In some situations, a single Laboratory test result archetype will contain multiple Specimen archetypes and multiple Genomic variant result archetypes. In these situations, this 'Specimen' data element is needed to be able to connect the results with the correct specimens., uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CHOICE, bindings=null, values=Choice of:
  •  Identifier
  •  URI
, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0098], code=at0098, itemType=SLOT, level=1, text=Additional details, description=Additional details to be captured., comment=null, uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=Include:
All not explicitly excluded archetypes, extendedValues=null]]}, 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=, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=null, extendedValues=null]}, addHierarchyItemsTo=items, currentHierarchyItemsForAdding=[ResourceSimplifiedHierarchyItem [path=/items[at0001], code=at0001, itemType=SLOT, level=1, text=Bioinformatic analysis workflow, description=Structured details about the bioinformatic analysis workflow or a link to a protocol., comment=null, uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=Include:
openEHR-EHR-CLUSTER.knowledge_base.v0 and specialisations Or
openEHR-EHR-CLUSTER.knowledge_base.v1 and specialisations Or
openEHR-EHR-CLUSTER.device.v1 and specialisations, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0002], code=at0002, itemType=SLOT, level=1, text=Reference genome, description=Structured details about the specific version of the human sequence assembly used for annotation., comment=For example, "GCF_000001405.38" Source name: NCBI Accession number: GCF_000001405 Version number: GCF_000001405.38 URL: https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.38/, uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=Include:
openEHR-EHR-CLUSTER.reference_sequence.v1 and specialisations, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0003], code=at0003, itemType=CLUSTER, level=1, text=Variant identifier, description=A reference to a specific variation recorded into a biological variation database., comment=For example: rs123456 (Identification) from dbSNP (Source name) version 151 (version). This internal cluster is repeatable to allow several different IDs from different databases for the same variant., uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=1..*, cardinalityText=, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0003]/items[at0004], code=at0004, itemType=ELEMENT, level=2, text=Source name, description=The name of the public data source that gives the variant identification., 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[at0003]/items[at0005], code=at0005, itemType=ELEMENT, level=2, text=Identification, description=The ID of a variation record., 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[at0003]/items[at0006], code=at0006, itemType=ELEMENT, level=2, text=Version, description=The exact version of the record., comment=null, 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[at0003]/items[at0007], code=at0007, itemType=ELEMENT, level=2, text=URL, description=A reference to a specific variation recorded into a biological variation database., comment=null, uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_URI, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0101], code=at0101, itemType=ELEMENT, level=1, text=Variant, description=Description of the variation at the genomic level following the HGVS nomenclature., comment=For example: "g.33038255C>A". If both this element and the "Structured variant" SLOT are used simultaneously, they need to represent identical data., uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_PARSABLE, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0045], code=at0045, itemType=SLOT, level=1, text=Structured variant, description=Structured description of the genomic variant., comment=This element is set to multiple occurrence to allow templates to be built with several different variant types allowed. However, when storing data, there should never be more than one CLUSTER archetype inserted here. If both this SLOT and the "Variant" data element are used simultaneously, they need to represent identical data., uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=Include:
openEHR-EHR-CLUSTER.repeated_sequence_variant.v0 and specialisations Or
openEHR-EHR-CLUSTER.inversion_variant.v0 and specialisations Or
openEHR-EHR-CLUSTER.substitution_variant.v0 and specialisations Or
openEHR-EHR-CLUSTER.indel_variant.v0 and specialisations Or
openEHR-EHR-CLUSTER.duplication_variant.v0 and specialisations Or
openEHR-EHR-CLUSTER.deletion_variant.v0 and specialisations Or
openEHR-EHR-CLUSTER.conversion_variant.v0 and specialisations Or
openEHR-EHR-CLUSTER.insertion_variant.v0 and specialisations Or
openEHR-EHR-CLUSTER.copy_number_variant.v0 and specialisations Or
openEHR-EHR-CLUSTER.translocation_variant.v0 and specialisations Or
openEHR-EHR-CLUSTER.repeated_sequence_variant.v1 and specialisations Or
openEHR-EHR-CLUSTER.inversion_variant.v1 and specialisations Or
openEHR-EHR-CLUSTER.substitution_variant.v1 and specialisations Or
openEHR-EHR-CLUSTER.indel_variant.v1 and specialisations Or
openEHR-EHR-CLUSTER.duplication_variant.v1 and specialisations Or
openEHR-EHR-CLUSTER.deletion_variant.v1 and specialisations Or
openEHR-EHR-CLUSTER.conversion_variant.v1 and specialisations Or
openEHR-EHR-CLUSTER.insertion_variant.v1 and specialisations Or
openEHR-EHR-CLUSTER.copy_number_variant.v1 and specialisations Or
openEHR-EHR-CLUSTER.translocation_variant.v1 and specialisations, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0008], code=at0008, itemType=CLUSTER, level=1, text=Transcript, description=Structured details about the transcript which is potentially affected by the variant., comment=null, uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=1..*, cardinalityText=, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0008]/items[at0009], code=at0009, itemType=SLOT, level=2, text=Transcript reference sequence, description=Structured details about the transcribed reference sequence., comment=Example: Source name: NCBI Accession number: NM_015557 Version number: NM_015557.2 URL: https://www.ncbi.nlm.nih.gov/nuccore/304361774, uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=[LOINC(2.65)::51958-7 | Transcript reference sequence [ID]], values=Include:
openEHR-EHR-CLUSTER.reference_sequence.v1 and specialisations, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0008]/items[at0010], code=at0010, itemType=ELEMENT, level=2, text=DNA region name, description=A human readable name for the region of interest., comment=For example: Exon number, intron number, splice site or other., uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_TEXT, bindings=[LOINC(2.65)::47999-8 | DNA region name [Identifier]], values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0008]/items[at0099], code=at0099, itemType=ELEMENT, level=2, text=Distance from splicing site, description=Distance in nucleotides between mutation and exon–intron junction., comment=null, 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]/items[at0011], code=at0011, itemType=ELEMENT, level=2, text=DNA change, description=Description of the variation at the DNA level following the HGVS nomenclature., comment=For example: "c.5249C>T"., uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_PARSABLE, bindings=[LOINC(2.65)::48004-6 | DNA change (c.HGVS)], values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0008]/items[at0012], code=at0012, itemType=ELEMENT, level=2, text=Amino acid change, description=Description of the variation at the protein level following the HGVS nomenclature., comment=For example: "p.T1750M"., uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_PARSABLE, bindings=[LOINC(2.65)::48005-3 | Amino acid change (pHGVS)], values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0008]/items[at0013], code=at0013, itemType=ELEMENT, level=2, text=Amino acid change type, description=Codified type for associated Amino Acid Marker., comment=null, uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CHOICE, bindings=[LOINC(2.65)::48006-1 | Amino acid change [Type]], values=Choice of:
  •  Coded Text
    • Wild type [The sequence at a given position is identical to the reference sequence.]
      [LOINC(2.65)::LA9658-1]
    • Deletion [A deletion in the amino acid sequence.]
      [LOINC(2.65)::LA6692-3]
    • Duplication [A duplication in the amino acid sequence.]
      [LOINC(2.65)::LA6686-5]
    • Frameshift [A frameshift in the amino acid sequence.]
      [LOINC(2.65)::LA6694-9]
    • Initiating methionine [A variant in a sequence affecting the translation initiation codon.]
      [LOINC(2.65)::LA6695-6]
    • Insertion [A insertion in the amino acid sequence.]
      [LOINC(2.65)::LA6687-3]
    • Insertion and deletion [An insertion/deletion in the amino acid sequence.]
      [LOINC(2.65)::LA9659-9]
    • Missense [A variant in a protein sequence where, compared to the reference sequence, one amino acid is replaced by another amino acid.]
      [LOINC(2.65)::LA6698-0]
    • Nonsense [A variant in a protein sequence where, compared to the reference sequence, an amino acid is replaced by a translational stop codon (termination codon).]
      [LOINC(2.65)::LA6699-8]
    • Silent [A variant in a DNA sequence that does not change the amino acid sequence of the encoded protein.]
      [LOINC(2.65)::LA6700-4]
    • Stop codon mutation [A variant in a sequence affecting the translational stop codon.]
      [LOINC(2.65)::LA6701-2]
  •  Text
, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0008]/items[at0100], code=at0100, itemType=ELEMENT, level=2, text=RNA change, description=Description of the variation at the RNA level following the HGVS nomenclature., comment=For example: "r.76a>u"., uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_PARSABLE, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0008]/items[at0015], code=at0015, itemType=CLUSTER, level=2, text=Predicted impact, description=Estimate of the effects that the variant may have on the transcript., comment=Calculation is based on a precise data source and only done by software. For example: If we have a CADD score of 30 for pathogenicity prediction, we’ll record: - Predicted Impact Analysis: CADD - Score: 30 - Qualitative prediction: probably damaging., uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=1..*, cardinalityText=, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0008]/items[at0015]/items[at0016], code=at0016, itemType=SLOT, level=3, text=Predicted impact analysis, description=Structured details about the tool used to calculate the predicted impact., comment=For example "CADD", "SIFT", etc., uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=Include:
openEHR-EHR-CLUSTER.knowledge_base.v0 and specialisations Or
openEHR-EHR-CLUSTER.knowledge_base.v1 and specialisations Or
openEHR-EHR-CLUSTER.device.v1 and specialisations, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0008]/items[at0015]/items[at0017], code=at0017, itemType=ELEMENT, level=3, text=Score, description=The calculated value., comment=null, uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=C_DV_QUANTITY, bindings=null, values=Property: Qualified real
Units:
, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0008]/items[at0015]/items[at0018], code=at0018, itemType=ELEMENT, level=3, text=Qualitative prediction, description=Human readable version of the predicted impact., comment=null, 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[at0008]/items[at0052], code=at0052, itemType=CLUSTER, level=2, text=Reported impact, description=Intepretation of the Mutation linked to a specific paper., comment=For example: activation, deactivating, dysfunction., uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=1..*, cardinalityText=, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0008]/items[at0052]/items[at0053], code=at0053, itemType=SLOT, level=3, text=Source, description=A reference to the specific research paper., 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.citation.v0 and specialisations Or
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  • First [First part of a Fusion Gene.]
  • Second [Second part of a Fusion Gene.]
, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0008]/items[at0058], code=at0058, itemType=ELEMENT, level=2, text=ACMG classification, description=Single DNA marker or individual allele interpretation in the context of the assessed genetic disease according to the ACMG recommendations., comment=null, uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_CODED_TEXT, bindings=[LOINC(2.65)::53037-8 | Genetic variation clinical significance [Imp]], values=
  • Pathogenic [Pathogenic variant.]
    [LOINC(2.65)::LA6668-3]
  • Likely pathogenic [Likely pathogenic variant.]
    [LOINC(2.65)::LA26332-9]
  • Uncertain significance [Variant of uncertain significance.]
    [LOINC(2.65)::LA26333-7]
  • Likely benign [Likely benign variant.]
    [LOINC(2.65)::LA26334-5]
  • Benign [Benign variant.]
    [LOINC(2.65)::LA6675-8]
, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0008]/items[at0059], code=at0059, itemType=ELEMENT, level=2, text=Fusion exon, description=The number of the exon which is either the end or the beginning of the fusion., comment=null, 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[at0023], code=at0023, itemType=ELEMENT, level=1, text=Best transcript candidate, description=The ID of the transcript with the highest predicted impact., comment=null, 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[at0024], code=at0024, itemType=CLUSTER, level=1, text=Conservation, description=Structured details about the evolutionary conservation., comment=null, uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=1..*, cardinalityText=, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0024]/items[at0025], code=at0025, itemType=SLOT, level=2, text=Conservation score analysis, description=Structured details about the tool used to calculate the conservation score., comment=For example "PhastCons7-way"., uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=Include:
openEHR-EHR-CLUSTER.knowledge_base.v0 and specialisations Or
openEHR-EHR-CLUSTER.knowledge_base.v1 and specialisations Or
openEHR-EHR-CLUSTER.device.v1 and specialisations, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0024]/items[at0026], code=at0026, itemType=ELEMENT, level=2, text=Score, description=The conservation score., comment=null, uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=C_DV_QUANTITY, bindings=null, values=Property: Qualified real
Units:
, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0060], code=at0060, itemType=ELEMENT, level=1, text=Read depth, description=Total number of reads mapped at this specific location., comment=null, 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[at0028], code=at0028, itemType=ELEMENT, level=1, text=Allele depth, description=The number of reads that support the reported variant., comment=null, 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[at0047], code=at0047, itemType=ELEMENT, level=1, text=Allele frequency, description=The relative frequency of an allele at a particular locus, expressed as a number from 0 to 1., comment=null, uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=C_DV_QUANTITY, bindings=[LOINC(2.65)::81258-6 | Allelic frequency [NFr]], values=Property: Qualified real
Units:
  • 0.0..1.0
, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0029], code=at0029, itemType=CLUSTER, level=1, text=Population allele frequency details, description=The relative frequency of a particular allele in the population, expressed as a number from 0 to 1., comment=null, uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=1..*, cardinalityText=, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0029]/items[at0030], code=at0030, itemType=SLOT, level=2, text=Population allele frequency analysis, description=Structured details about the database used to calculate the allele frequency., comment=null, uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=Include:
openEHR-EHR-CLUSTER.knowledge_base.v0 and specialisations Or
openEHR-EHR-CLUSTER.knowledge_base.v1 and specialisations Or
openEHR-EHR-CLUSTER.device.v1 and specialisations, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0029]/items[at0031], code=at0031, itemType=ELEMENT, level=2, text=Population allele frequency, description=The population allele frequency., comment=null, uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=C_DV_QUANTITY, bindings=[LOINC(2.65)::81258-6 | Allelic frequency [NFr]], values=Property: Qualified real
Units:
  • 0.0..1.0
, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0061], code=at0061, itemType=CLUSTER, level=1, text=VCF quality filter, description=Structured details about the quality filters that have been applied to the data., comment=This field is derived from the FILTER column of VCF. , uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=1..*, cardinalityText=, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0061]/items[at0062], code=at0062, itemType=ELEMENT, level=2, text=Filter name, description=Name of the quality filter., comment=For example "q10"., 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[at0061]/items[at0063], code=at0063, itemType=ELEMENT, level=2, text=Description, description=Quality filter extended description., comment=For example "at this site the quality is below 10"., 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[at0061]/items[at0064], code=at0064, itemType=ELEMENT, level=2, text=Filter passed, description=Whether the variant passed the quality filter., comment=Record as True if the filter was passed., uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_BOOLEAN, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0067], code=at0067, itemType=ELEMENT, level=1, text=Strand bias ratio, description=The ratio of the strand bias., comment=null, uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=C_DV_QUANTITY, bindings=null, values=Property: Qualified real
Units:
, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0068], code=at0068, itemType=ELEMENT, level=1, text=Strand bias p-value, description=The Phred-scaled p-value of the strand bias., comment=null, uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=C_DV_QUANTITY, bindings=null, values=Property: Qualified real
Units:
, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0039], code=at0039, itemType=ELEMENT, level=1, text=Genotype, description=Genotype encoded as allele values separated by either of / or | (0 for the reference allele, 1 for the first alternate, etc.)., 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[at0040], code=at0040, itemType=ELEMENT, level=1, text=Allelic state, description=The level of occurrence of a single DNA Marker within a set of chromosomes., comment=This is the human readable version of genotype, e.g.: Heterozygous, Homozygous., uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CHOICE, bindings=[LOINC(2.65)::53034-5 | Allelic state], values=Choice of:
  •  Coded Text
    • Heteroplasmic [Heteroplasmic.]
      [LOINC(2.65)::LA6703-8]
    • Homoplasmic [Homoplasmic.]
      [LOINC(2.65)::LA6704-6]
    • Homozygous [Homozygous.]
      [LOINC(2.65)::LA6705-3]
    • Heterozygous [Heterozygous.]
      [LOINC(2.65)::LA6706-1]
    • Hemizygous [Hemizygous.]
      [LOINC(2.65)::LA6707-9]
  •  Text
, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0041], code=at0041, itemType=ELEMENT, level=1, text=Genotype quality, description=Conditional genotype quality, encoded as a phred quality., comment=null, uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_COUNT, bindings=null, values=min: >=0

, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0069], code=at0069, itemType=ELEMENT, level=1, text=Genotype probability, description=A comma separated list of the log10-scaled genotype likelihoods for all possible genotypes, given the reference and the alternate alleles., comment=null, 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[at0070], code=at0070, itemType=ELEMENT, level=1, text=Specimen identifier, description=Identification of the specimen used for the genomic result., comment=In some situations, a single Laboratory test result archetype will contain multiple Specimen archetypes and multiple Genomic variant result archetypes. In these situations, this 'Specimen' data element is needed to be able to connect the results with the correct specimens., uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CHOICE, bindings=null, values=Choice of:
  •  Identifier
  •  URI
, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0098], code=at0098, itemType=SLOT, level=1, text=Additional details, description=Additional details to be captured., comment=null, uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=Include:
All not explicitly excluded archetypes, extendedValues=null]], minIndents={}, termBindingRetrievalErrorMessage=null]