ARCHETYPE ID | openEHR-EHR-CLUSTER.genomic_variant_result.v1 |
Concept | Genomic variant result |
Description | Findings and annotations related to one variant found in a human individual by a sequencing test. |
Use | Use to report findings and annotations related to one variant found in the genome by a sequencing test. This archetype has been designed to be nested in the 'Test result' SLOT within the OBSERVATION.laboratory_test_result archetype. It is intended to provide a consistent framework for nesting any specific genomic variant CLUSTER archetype within the 'Structured variant' SLOT. 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. |
Misuse | Not to be used for recording information about the comparison of several samples. Use a specific archetype for this purpose. |
Purpose | To report findings and annotations related to one variant found in the genome by a sequencing test. |
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 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 |
Authors | Author name: Cecilia Mascia Organisation: CRS4, Italy Email: cecilia.mascia@crs4.it Date originally authored: 2019-01-15 |
Other Details Language | Author 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 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 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.openehr, custodian_namespace=org.openehr, original_publisher=openEHR Foundation, MD5-CAM-1.0.1=8D6BEB38EDABF7F358821E8EA5B84DB9, build_uid=6a69501f-0a41-47db-8056-bcdc30bdfc86, revision=1.0.3} |
Keywords | variation, VCF, variant, genetic, genomic, variant calling, sequence, mutation, allele, genotype |
Lifecycle | published |
UID | ddb13dc5-5227-48f7-93f5-1b6825ace295 |
Language used | en |
Citeable Identifier | 1246.145.399 |
Revision Number | 1.0.3 |
All | Archetype [runtimeNameConstraintForConceptName=null, archetypeConceptBinding=null, archetypeConceptDescription=Findings and annotations related to one variant found in a human individual by a sequencing test., 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=
openEHR-EHR-CLUSTER.knowledge_ 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_ openEHR-EHR-CLUSTER.knowledge_ openEHR-EHR-CLUSTER.genomic_ openEHR-EHR-CLUSTER.genomic_ openEHR-EHR-CLUSTER.genomic_ openEHR-EHR-CLUSTER.genomic_ openEHR-EHR-CLUSTER.genomic_ openEHR-EHR-CLUSTER.genomic_ openEHR-EHR-CLUSTER.genomic_ openEHR-EHR-CLUSTER.genomic_ openEHR-EHR-CLUSTER.genomic_ openEHR-EHR-CLUSTER.genomic_ openEHR-EHR-CLUSTER.genomic_ openEHR-EHR-CLUSTER.reference_
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, 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=For example: 'ENST00000413998.7'., 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 knowledge base, description=Structured details about the reference 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_ 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=The 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=min: >=0 , 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=min: >=0 , 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., comment=For example: '0.63'., uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=C_DV_QUANTITY, bindings=[LOINC(2. 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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=Did the variant pass 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., comment=The format for the genotype should be value separated by either of / or | (0 for the reference allele, 1 for the first alternate, etc.). For example: '1 | 0' or '0/0/1'., 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[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.
, 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 OBSERVATION.laboratory_test_result archetype will contain multiple CLUSTER.specimen archetypes and multiple CLUSTER.genomic_variant_result archetypes. In these situations, this 'Specimen identifier' 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:
All not explicitly excluded archetypes, extendedValues=null]], content=[], description=[], contacts=[], state=[], events=[], provider=[], identities=[], protocol=[]}, 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 the protocol that is used., 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_ 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_ openEHR-EHR-CLUSTER.knowledge_ openEHR-EHR-CLUSTER.genomic_ openEHR-EHR-CLUSTER.genomic_ openEHR-EHR-CLUSTER.genomic_ openEHR-EHR-CLUSTER.genomic_ openEHR-EHR-CLUSTER.genomic_ openEHR-EHR-CLUSTER.genomic_ openEHR-EHR-CLUSTER.genomic_ openEHR-EHR-CLUSTER.genomic_ openEHR-EHR-CLUSTER.genomic_ openEHR-EHR-CLUSTER.genomic_ openEHR-EHR-CLUSTER.genomic_ openEHR-EHR-CLUSTER.reference_
openEHR-EHR-CLUSTER.knowledge_ 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=For example: '30.2'., 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=For example: 'probably damaging'., 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=Functional impact, description=Interpretation of the variation linked to a specific paper., 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[at0052]/items[at0054], code=at0054, itemType=ELEMENT, level=3, text=Impact, description=Single word or phrase describing the reported impact of the specific variant., comment=For example: 'activating', 'deactivating', 'dysfunction', 'gain of function'. Coding with a terminology is preferred, where possible., 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[at0052]/items[at0053], code=at0053, itemType=SLOT, level=3, text=Source, description=The 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[at0019], code=at0019, itemType=CLUSTER, level=2, text=Gene, description=Structured details about the gene carrying 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=Gene name, description=The full gene name approved by the HGNC that conveys 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=
, 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=For example: 'ENST00000413998.7'., 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 knowledge base, description=Structured details about the reference 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_ 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=The 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=min: >=0 , 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=min: >=0 , 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., comment=For example: '0.63'., uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=C_DV_QUANTITY, bindings=[LOINC(2. 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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=Did the variant pass 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., comment=The format for the genotype should be value separated by either of / or | (0 for the reference allele, 1 for the first alternate, etc.). For example: '1 | 0' or '0/0/1'., 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[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.
, 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 OBSERVATION.laboratory_test_result archetype will contain multiple CLUSTER.specimen archetypes and multiple CLUSTER.genomic_variant_result archetypes. In these situations, this 'Specimen identifier' 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:
All not explicitly excluded archetypes, extendedValues=null]], minIndents={}, termBindingRetrievalErrorMessage=null] |