ARCHETYPE General sequencing result parameter (openEHR-EHR-CLUSTER.general_sequencing_result_parameter.v0)

ARCHETYPE IDopenEHR-EHR-CLUSTER.general_sequencing_result_parameter.v0
ConceptGeneral sequencing result parameter
DescriptionGeneral sequencing result parameter.
UseUse to report general sequencing result parameter determined for 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.
MisuseNot to be used to report genetic variants, but only general parameters that are determined once per sequencing run.
PurposeTo record general sequencing result parameter of a performed sequencing test.
References
AuthorsAuthor name: Aurelie Tomczak
Organisation: Institute of Pathology, University Hospital Heidelberg
Email: au.tomczak@yahoo.com
Date originally authored: 2020-07-17
Other Details LanguageAuthor name: Aurelie Tomczak
Organisation: Institute of Pathology, University Hospital Heidelberg
Email: au.tomczak@yahoo.com
Date originally authored: 2020-07-17
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=HiGHmed, original_namespace=org.openehr, original_publisher=openEHR Foundation, custodian_namespace=org.highmed, MD5-CAM-1.0.1=D29DAAA9079EEC0DC606871E6266F676, build_uid=d42de821-caab-46a8-93d2-01a84b34d20e, revision=0.0.1-alpha}
KeywordsTumor cell content, BRCAness, Microsatellite instability (MSI), Tumor Mutational Burden (TMB) per Mb, Sequencing result parameter, Whole genome sequencing, Targeted sequencing
Lifecyclein_development
UID662cbae0-6ab8-4ad9-a847-547e69b5c356
Language useden
Citeable Identifier1246.145.1291
Revision Number0.0.1-alpha
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, subjectOfData=unconstrained, archetypeTranslationTree=null, topLevelToAshis={source=[], capabilities=[], contacts=[], items=[ResourceSimplifiedHierarchyItem [path=/items[at0001], code=at0001, itemType=ELEMENT, level=1, text=Sequenced tissue type, description=Normal vs. tumor sample., comment=null, uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CHOICE, bindings=null, values=Choice of:
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    • Normal tissue [Identifies germline mutations.]
    • Tumor tissue [Identifies somatic mutations.]
  •  Text
, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0004], code=at0004, itemType=ELEMENT, level=1, text=Tumor cell content (pathologic/histologic), description=Tumor cell content determinded by pathologic/histologic methods., comment=null, uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CHOICE, bindings=null, values=Choice of:
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, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0005], code=at0005, itemType=ELEMENT, level=1, text=Tumor cell content (bioinformatic), description=Tumor cell content determinded by bioinformatic methods., comment=null, uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CHOICE, bindings=null, values=Choice of:
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, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0007], code=at0007, itemType=ELEMENT, level=1, text=Microsatellite instability (MSI), description=Microsatellite instability (MSI)., 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; max: <=2

, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0006], code=at0006, itemType=ELEMENT, level=1, text=Tumor Mutational Burden (TMB) per Mb, description=Tumor Mutational Burden (TMB) per Megabase., 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], code=at0008, itemType=ELEMENT, level=1, text=BRCAness, description=BRCAness is defined as a phenotypic copy of germline BRCA mutations., 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; max: <=1

, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0009], code=at0009, itemType=CLUSTER, level=1, text=Further result parameter, description=Cluster to include additional result parameter not already defined above., 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[at0009]/items[at0013], code=at0013, itemType=ELEMENT, level=2, text=Parameter name, description=Parameter name., comment=null, uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CHOICE, bindings=null, values=Choice of:
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    • Normal tissue [Identifies germline mutations.]
    • Tumor tissue [Identifies somatic mutations.]
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, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0004], code=at0004, itemType=ELEMENT, level=1, text=Tumor cell content (pathologic/histologic), description=Tumor cell content determinded by pathologic/histologic methods., comment=null, uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CHOICE, bindings=null, values=Choice of:
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, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0005], code=at0005, itemType=ELEMENT, level=1, text=Tumor cell content (bioinformatic), description=Tumor cell content determinded by bioinformatic methods., comment=null, uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CHOICE, bindings=null, values=Choice of:
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, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0007], code=at0007, itemType=ELEMENT, level=1, text=Microsatellite instability (MSI), description=Microsatellite instability (MSI)., 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; max: <=2

, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0006], code=at0006, itemType=ELEMENT, level=1, text=Tumor Mutational Burden (TMB) per Mb, description=Tumor Mutational Burden (TMB) per Megabase., 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], code=at0008, itemType=ELEMENT, level=1, text=BRCAness, description=BRCAness is defined as a phenotypic copy of germline BRCA mutations., 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; max: <=1

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