ARCHETYPE Pharmacogenetic analyte result (openEHR-EHR-CLUSTER.pharmacogenetic_analyte_result.v0)

ARCHETYPE IDopenEHR-EHR-CLUSTER.pharmacogenetic_analyte_result.v0
ConceptPharmacogenetic analyte result
DescriptionDetails of the result of pharmacogenetic testing against a single gene, including the detected genotype, pharmacognetic phenotype, activity score to support prescribing decision support.
UseThe key use of this archetype is to record the results of pharmacogenetic testing to support clinical decision making, including digital prescribing decision support, commonly as part of a panel of similar results. It would commonly be carried inside the OBSERVATION.laboratory_test_result archetype, replacing , or perhaps alongside the CLUSTER.laboratory_analyte_result archetype, depending on exact laboratory reporting practice. Typically this testing is performed by testing for specific allele variations at a specific gene location, adding derived phenotypic information such as metaboliser status and activity score from which specific therapeutic implications may be drawn. Although some laboratory reports incorporate those therapeutic recommendations, these are explicitly intended to be carried in separate Genomic Therapeutic implication archetype. The principal reason is that those implications will change over time as new research emerges. A further issue is that each individual result may only cover a partial set of all known testable alleles for a specific gene, which means that the the full genotype and related pharmacogenetic phenotype may need to updated as further testing is done. Discussion is ongoing at to whether that 'cumulative result' is best derived dynamically from existing results , or whether a specific 'cumulative result' should be maintained as a separate record, probably as an Evaluation archetype, and updated as new individual results are obtained. The design was heavily influenced by the HL7 FHIR Genomics Reporting Implementation Guide and CPIC(http://cpicpgx.org/) guidance on reporting and terminology bindings.
MisuseThis archetype is not intended to support other types of genomic analysis / beyond pharmacogenetics, such as molecular pathology reporting.
PurposeTo record the details of the result of pharmacogenetic testing against a single gene, including the detected genotype, pharmacognetic phenotype, activity score to support prescribing decision support.
ReferencesHL7.FHIR.UV.GENOMICS-REPORTING\Genomics Background - FHIR v4.0.1 "HL7.FHIR.UV.GENOMICS-REPORTING\Genomics Background - FHIR V4.0.1". Build.Fhir.Org, 2023, http://build.fhir.org/ig/HL7/genomics-reporting/background.html. Accessed 7 Mar 2023.

Dolin, R., Boxwala, A. and Shalaby, J. Dolin, R.H. et al. "A Pharmacogenomics Clinical Decision Support Service Based On FHIR And CDS Hooks". Methods Of Information In Medicine, vol 57, no. S 02, 2018, pp. e115-e123. Georg Thieme Verlag KG, doi:10.1055/s-0038-1676466. Accessed 7 Mar 2023.

Cpicpgx.Org, 2023, http://cpicpgx.org/wp-content/uploads/2016/02/CPIC-Term-Standardization-and-LOINC-151203.pdf. Accessed 22 May 2023.
Copyright© openEHR Foundation
AuthorsAuthor name: Ian McNicoll
Organisation: freshEHR Clinical Informatics
Email: ian@freshEHR.com
Date originally authored: 2023-05-22
Other Details LanguageAuthor name: Ian McNicoll
Organisation: freshEHR Clinical Informatics
Email: ian@freshEHR.com
Date originally authored: 2023-05-22
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=Apperta UK, references=HL7.FHIR.UV.GENOMICS-REPORTING\Genomics Background - FHIR v4.0.1 "HL7.FHIR.UV.GENOMICS-REPORTING\Genomics Background - FHIR V4.0.1". Build.Fhir.Org, 2023, http://build.fhir.org/ig/HL7/genomics-reporting/background.html. Accessed 7 Mar 2023. Dolin, R., Boxwala, A. and Shalaby, J. Dolin, R.H. et al. "A Pharmacogenomics Clinical Decision Support Service Based On FHIR And CDS Hooks". Methods Of Information In Medicine, vol 57, no. S 02, 2018, pp. e115-e123. Georg Thieme Verlag KG, doi:10.1055/s-0038-1676466. Accessed 7 Mar 2023. Cpicpgx.Org, 2023, http://cpicpgx.org/wp-content/uploads/2016/02/CPIC-Term-Standardization-and-LOINC-151203.pdf. Accessed 22 May 2023., current_contact=Ian McNicoll (ian@freshehr.com>, original_namespace=org.openehr, original_publisher=openEHR International, custodian_namespace=uk.org.clinicalmodels, MD5-CAM-1.0.1=3A006A158FDD5B208A9CBCE5E1BF0280, build_uid=84ca568d-e093-4d7f-a57b-1cd95c7553cd, ip_acknowledgements=This artefact includes content from SNOMED Clinical Terms® (SNOMED CT®) which is copyrighted material of the International Health Terminology Standards Development Organisation (IHTSDO). Where an implementation of this artefact makes use of SNOMED CT content, the implementer must have the appropriate SNOMED CT Affiliate license - for more information contact https://www.snomed.org/snomed-ct/get-snomed or info@snomed.org., revision=0.0.1-alpha}
Keywordspharmacogenetics, laboratory, enzyme, medication, pgx, CPIC, recommendation, genomics
Lifecyclein_development
UID594a2f90-6a64-4fc1-8578-066a25a938d0
Language useden
Citeable Identifier1013.1.7066
Revision Number0.0.1-alpha
AllArchetype [runtimeNameConstraintForConceptName=null, archetypeConceptBinding=null, archetypeConceptDescription=Details of the result of pharmacogenetic testing against a single gene, including the detected genotype, pharmacognetic phenotype, activity score to support prescribing decision support., archetypeConceptComment=null, otherContributors=John McDermott, University of Manchester
Videha Sharma, University of Manchester
Jessica Keen, North West Genomic Medicine Service Alliance, originalLanguage=en, translators=, subjectOfData=unconstrained, archetypeTranslationTree=null, topLevelToAshis={details=[], description=[], activities=[], target=[], credentials=[], data=[], items=[ResourceSimplifiedHierarchyItem [path=/items[at0003], code=at0003, itemType=ELEMENT, level=1, text=Gene name, description=A term which identifies the gene concerned., comment=Preferably this should be coded with terms from the HGNC nomenclature (HUGO Gene Nomenclature Committee). For example: 'http://www.genenames.org::CYP2C9 | CYP2C9 |' See https://terminology.hl7.org/CodeSystem-v3-hgnc.json.html Note that CPIC currently recommends the use of LOINC-based "Phenotypic interpretation" terms and not the Gene names, e.g. "TPMT Gene Product Metabolic Activity Interpretation"., 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[at0004], code=at0004, itemType=ELEMENT, level=1, text=Diplotype, description=A textual representation of the diplotype, normally as string of characters, either as as gene change descriptors or star allele diplotypes., comment=For example: 'g.94938683A>G' (Gene changes) '*1/*36' (Star allele diplotype)., 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[at0052], code=at0052, itemType=ELEMENT, level=1, text=Phenotype, description=The estimated pharmacological impact of the identified genotype., comment=The internal terms are based on CPIC phenotype recommendations - see https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5253119/ . For example: 'local::at0057 | Poor metaboliser |' These terms are bound to SNOMED CT and LOINC equivalents. The list is left open as other terms may be required., uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CHOICE, bindings=null, values=Choice of:
  •  Coded Text
    • Normal metaboliser [The metaboliser status is normal.]
      [SNOMED-CT::3351000181105]
      [LOINC::LA25391-6]
    • Rapid metaboliser [The metaboliser status is rapid.]
      [SNOMED-CT::3341000181107]
      [LOINC::LA25390-8]
    • Ultrarapid metaboliser [The metaboliser status is ultrarapid.]
      [SNOMED-CT::3331000181100]
      [LOINC::LA10315-2]
    • Intermediate metaboliser [The metaboliser status is intermediate.]
      [SNOMED-CT::3361000181108]
      [LOINC::LA10317-8]
    • Poor metaboliser [The metaboliser status is poor.]
      [SNOMED-CT::3371000181103]
      [LOINC::LA9657-3]
    • Increased function [Functional activity is increased.]
      [SNOMED-CT::3381000181101]
      [LOINC::LA25392-4]
    • Decreased function [Functional activity is decreased.]
      [SNOMED-CT::3401000181101]
      [LOINC::LA25395-7]
    • Normal function [Functional activity is normal.]
      [SNOMED-CT::3391000181104]
      [LOINC::LA25393-2]
    • Poor function [Functional activity is poor.]
      [SNOMED-CT::3451000181100]
      [LOINC::LA25394-0]
    • Negative [Negative test for risk alleles.]
      [SNOMED-CT::260385009 | Negative]
      [LOINC::LA6576-8]
    • Positive [Positive test for risk alleles.]
      [SNOMED-CT::10828004 | Positive]
      [LOINC::LA6577-6]
    • Normal risk of aminoglycoside-induced hearing loss [Normal risk of aminoglycoside-induced hearing loss.]
    • Increased risk of aminoglycoside-induced hearing loss [Increased risk of aminoglycoside-induced hearing loss.]
    • Uncertain risk of aminoglycoside-induced hearing loss [Uncertain risk of aminoglycoside-induced hearing loss.]
  •  Text
, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0080], code=at0080, itemType=ELEMENT, level=1, text=Overall activity score, description=An associated derived activity score, based on known association with specific genotypes and individual allele activity values, which is required to assess metaboliser status for some phenotypes., 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: >=0.0 , extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0084], code=at0084, itemType=CLUSTER, level=1, text=Individual activity value, description=A list of enzyme activity values each associated with a specific allele, which are used to derive the Overall activity score., 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[at0084]/items[at0086], code=at0086, itemType=ELEMENT, level=2, text=Allele, description=The allele descriptor associated with the activity value., comment=For example: '*36'., 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[at0084]/items[at0085], code=at0085, itemType=ELEMENT, level=2, text=Activity value, description=An associated derived activity score, based on known association with specific genotypes, which is required to assess metaboliser status for some phenotypes., comment=For example: '0.5'., 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: >=0.0 , extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0075], code=at0075, itemType=CLUSTER, level=1, text=Per-allele tested, description=A list of the specific alleles tested by this pharmacogenetic test, as the specific alleles may vary between tests., 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[at0075]/items[at0078], code=at0078, itemType=ELEMENT, level=2, text=SNP rsNumber, description=The rsNumber (rs ID) of the allele tested, based on the the dbSNP identifier using terminology ID 'http://terminology.hl7.org/NamingSystem/v3-dbSNP'., comment=For example: 'http://terminology.hl7.org/NamingSystem/v3-dbSNP::rs3918290 | rs3918290 |'., 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[at0075]/items[at0083], code=at0083, itemType=ELEMENT, level=2, text=Reference allele, description=A text descriptor of the expected reference content of the tested allele., comment=For example: 'A/A'., 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[at0075]/items[at0082], code=at0082, itemType=ELEMENT, level=2, text=Detected allele, description=A text descriptor of the detected content of the tested allele., comment=For example: 'A/G'., 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[at0075]/items[at0096], code=at0096, itemType=SLOT, level=2, text=Variant detail, description=Details of variant findings., comment=null, uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=Include:
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openEHR-EHR-CLUSTER.simple_variant.v0, extendedValues=null]], provider=[], ism_transition=[], context=[], events=[], content=[], source=[], state=[], capabilities=[], contacts=[], relationships=[], protocol=[], other_participations=[], identities=[]}, 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[at0003], code=at0003, itemType=ELEMENT, level=1, text=Gene name, description=A term which identifies the gene concerned., comment=Preferably this should be coded with terms from the HGNC nomenclature (HUGO Gene Nomenclature Committee). For example: 'http://www.genenames.org::CYP2C9 | CYP2C9 |' See https://terminology.hl7.org/CodeSystem-v3-hgnc.json.html Note that CPIC currently recommends the use of LOINC-based "Phenotypic interpretation" terms and not the Gene names, e.g. "TPMT Gene Product Metabolic Activity Interpretation"., 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[at0004], code=at0004, itemType=ELEMENT, level=1, text=Diplotype, description=A textual representation of the diplotype, normally as string of characters, either as as gene change descriptors or star allele diplotypes., comment=For example: 'g.94938683A>G' (Gene changes) '*1/*36' (Star allele diplotype)., 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[at0052], code=at0052, itemType=ELEMENT, level=1, text=Phenotype, description=The estimated pharmacological impact of the identified genotype., comment=The internal terms are based on CPIC phenotype recommendations - see https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5253119/ . For example: 'local::at0057 | Poor metaboliser |' These terms are bound to SNOMED CT and LOINC equivalents. The list is left open as other terms may be required., uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CHOICE, bindings=null, values=Choice of:
  •  Coded Text
    • Normal metaboliser [The metaboliser status is normal.]
      [SNOMED-CT::3351000181105]
      [LOINC::LA25391-6]
    • Rapid metaboliser [The metaboliser status is rapid.]
      [SNOMED-CT::3341000181107]
      [LOINC::LA25390-8]
    • Ultrarapid metaboliser [The metaboliser status is ultrarapid.]
      [SNOMED-CT::3331000181100]
      [LOINC::LA10315-2]
    • Intermediate metaboliser [The metaboliser status is intermediate.]
      [SNOMED-CT::3361000181108]
      [LOINC::LA10317-8]
    • Poor metaboliser [The metaboliser status is poor.]
      [SNOMED-CT::3371000181103]
      [LOINC::LA9657-3]
    • Increased function [Functional activity is increased.]
      [SNOMED-CT::3381000181101]
      [LOINC::LA25392-4]
    • Decreased function [Functional activity is decreased.]
      [SNOMED-CT::3401000181101]
      [LOINC::LA25395-7]
    • Normal function [Functional activity is normal.]
      [SNOMED-CT::3391000181104]
      [LOINC::LA25393-2]
    • Poor function [Functional activity is poor.]
      [SNOMED-CT::3451000181100]
      [LOINC::LA25394-0]
    • Negative [Negative test for risk alleles.]
      [SNOMED-CT::260385009 | Negative]
      [LOINC::LA6576-8]
    • Positive [Positive test for risk alleles.]
      [SNOMED-CT::10828004 | Positive]
      [LOINC::LA6577-6]
    • Normal risk of aminoglycoside-induced hearing loss [Normal risk of aminoglycoside-induced hearing loss.]
    • Increased risk of aminoglycoside-induced hearing loss [Increased risk of aminoglycoside-induced hearing loss.]
    • Uncertain risk of aminoglycoside-induced hearing loss [Uncertain risk of aminoglycoside-induced hearing loss.]
  •  Text
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.* or
openEHR-EHR-CLUSTER.simple_variant.v0, extendedValues=null]], minIndents={}, termBindingRetrievalErrorMessage=null]