ARCHETYPE Pharmacogenetic result (openEHR-EHR-CLUSTER.pharmacogenetic_result.v0)

ARCHETYPE IDopenEHR-EHR-CLUSTER.pharmacogenetic_result.v0
ConceptPharmacogenetic result
DescriptionFindings on pharmacogenetic testing for a single gene.
UseUse to record findings on pharmacogenetic testing for a single gene. The primary intended use of this archetype is to support clinical decision making, including digital prescribing decision support, commonly as part of a panel of similar results. It would normally be carried within the CLUSTER.laboratory_analyte_result archetype. 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 as 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. The design was heavily influenced by CPIC (http://cpicpgx.org/) guidance on reporting and terminology bindings. Pharmacogenetic laboratory reporting and messaging is highly variable, but we have taken account of emerging work in this field from the HL7 FHIR Genomics Reporting Implementation Guide. Pharmacogenetic reporting is generally recognised to be more clinically focused than other areas, such as cancer genomics, which are covered by the openEHR Genomics project archetypes. Through discussions with the primary authors of these archetypes, we have attempted to ensure maximal alignment and identified the appropriate use in the pharmacogenetic context.
MisuseNot to be used for recording information about genomic variants beyond the scope of interactions between an identified gene and a medication. Use specific genomics archetypes for purposes other than pharmacogenetics.
PurposeTo record findings on pharmacogenetic testing for a single gene.
ReferencesHL7 FHIR. Genomic Background. [Internet]. HL7 FHIR; 2024. Available from: http://build.fhir.org/ig/HL7/genomics-reporting/background.html.

Dolin RH, Boxwala A, Shalaby J. A Pharmacogenomics Clinical Decision Support Service Based on FHIR and CDS Hooks. Methods Inf Med. 2018 Dec;57(S 02):e115-e123. doi: 10.1055/s-0038-1676466. Epub 2019 Jan 3. PubMed PMID: 30605914.

Freimuth RR. CPIC Term Standardization: LOINC Codes. [Internet]. CPIC; 2015 December. Available from: https://cpicpgx.org/wp-content/uploads/2016/02/CPIC-Term-Standardization-and-LOINC-151203.pdf.

McDermott JH, Wright S, Sharma V, Newman WG, Payne K, Wilson P. Characterizing pharmacogenetic programs using the consolidated framework for implementation research: A structured scoping review. Front Med (Lausanne). 2022;9:945352. doi: 10.3389/fmed.2022.945352. eCollection 2022. PubMed PMID: 36059837; PubMed Central PMCID: PMC9433561.

Roosan D, Hwang A, Law AV, Chok J, Roosan MR. The inclusion of health data standards in the implementation of pharmacogenomics systems: a scoping review. Pharmacogenomics. 2020 Nov;21(16):1191-1202. doi: 10.2217/pgs-2020-0066. Epub 2020 Oct 30. Review. PubMed PMID: 33124487.

Global Alliance for Genomics and Health. Variation Representation (VRS). [Internet]. Global Alliance for Genomics and Health; 2024. Available from: https://www.ga4gh.org/product/variation-representation/.
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. Genomic Background. [Internet]. HL7 FHIR; 2024. Available from: http://build.fhir.org/ig/HL7/genomics-reporting/background.html. Dolin RH, Boxwala A, Shalaby J. A Pharmacogenomics Clinical Decision Support Service Based on FHIR and CDS Hooks. Methods Inf Med. 2018 Dec;57(S 02):e115-e123. doi: 10.1055/s-0038-1676466. Epub 2019 Jan 3. PubMed PMID: 30605914. Freimuth RR. CPIC Term Standardization: LOINC Codes. [Internet]. CPIC; 2015 December. Available from: https://cpicpgx.org/wp-content/uploads/2016/02/CPIC-Term-Standardization-and-LOINC-151203.pdf. McDermott JH, Wright S, Sharma V, Newman WG, Payne K, Wilson P. Characterizing pharmacogenetic programs using the consolidated framework for implementation research: A structured scoping review. Front Med (Lausanne). 2022;9:945352. doi: 10.3389/fmed.2022.945352. eCollection 2022. PubMed PMID: 36059837; PubMed Central PMCID: PMC9433561. Roosan D, Hwang A, Law AV, Chok J, Roosan MR. The inclusion of health data standards in the implementation of pharmacogenomics systems: a scoping review. Pharmacogenomics. 2020 Nov;21(16):1191-1202. doi: 10.2217/pgs-2020-0066. Epub 2020 Oct 30. Review. PubMed PMID: 33124487. Global Alliance for Genomics and Health. Variation Representation (VRS). [Internet]. Global Alliance for Genomics and Health; 2024. Available from: https://www.ga4gh.org/product/variation-representation/., 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=112688B395B83DBD5A9FFD327ACB5FA7, build_uid=9b8f4de3-aeab-4a6d-895b-81db6934534c, 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, genomics, pharmacogenomics, genotype
Lifecyclein_development
UIDb358a419-3739-4068-886b-a687edd75b5d
Language useden
Citeable Identifier1013.1.7066
Revision Number0.0.1-alpha
AllArchetype [runtimeNameConstraintForConceptName=null, archetypeConceptBinding=null, archetypeConceptDescription=Findings on pharmacogenetic testing for a single gene., 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={items=[ResourceSimplifiedHierarchyItem [path=/items[at0003], code=at0003, itemType=ELEMENT, level=1, text=Gene symbol, description=The official gene symbol approved by the HGNC, which is a short abbreviated form of the gene name., comment=Coding with an external terminology is preferred, where possible. Preferably this should be coded with terms from the HGNC (HUGO Gene Nomenclature Committee) nomenclature, using 'http://www.genenames.org' as the terminology identifier. For example: 'http://www.genenames.org::CYP2C9 | CYP2C9 |'., 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[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) or '*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 coded text values are based on CPIC phenotype recommendations - see https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5253119/. It is possible to add other coded text values when they are 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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  •  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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openEHR-EHR-CLUSTER.knowledge_base_reference.v1, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0096], code=at0096, itemType=SLOT, level=1, text=Variant detail, description=Details of variant findings., 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.genomic_variant_result.v1, extendedValues=null]], minIndents={}, termBindingRetrievalErrorMessage=null]