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FHIR-genomics-reporting.xml
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FHIR-genomics-reporting.xml
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<?xml version="1.0" encoding="UTF-8"?>
<specification xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" ballotUrl="http://hl7.org/fhir/uv/genomics-reporting/2021May" ciUrl="http://build.fhir.org/ig/HL7/genomics-reporting" defaultVersion="1.0.0" defaultWorkgroup="cg" gitUrl="https://github.com/HL7/genomics-reporting" url="http://hl7.org/fhir/uv/genomics-reporting">
<version code="current" url="http://build.fhir.org/ig/HL7/genomics-reporting"/>
<version code="1.1.0" url="http://hl7.org/fhir/uv/genomics-reporting/2021May"/>
<version code="1.0.0" url="http://hl7.org/fhir/uv/genomics-reporting/STU1"/>
<version code="0.3.0" deprecated="true" url="http://hl7.org/fhir/uv/genomics-reporting/2019Jan"/>
<version code="0.1.0" deprecated="true" url="http://hl7.org/fhir/uv/genomics-reporting/2018May"/>
<version code="1.0" deprecated="true" url="http://hl7.org/fhir/uv/genomics-reporting/STU1"/>
<artifactPageExtension value="-definitions"/>
<artifactPageExtension value="-examples"/>
<artifactPageExtension value="-mappings"/>
<artifact deprecated="true" key="Feed" name="Bundle"/>
<artifact id="ConceptMap/dna-change-type-map" key="ConceptMap-dna-change-type-map" name="Concept mapping for DNA Change Type"/>
<artifact deprecated="true" id="CodeSystem/ConditionInheritanceMode" key="CodeSystem-ConditionInheritanceMode" name="Condition Inheritance Pattern"/>
<artifact id="CodeSystem/condition-inheritance-mode-cs" key="CodeSystem-ConditionInheritanceModeCS" name="Condition Inheritance Pattern Codes"/>
<artifact id="ValueSet/condition-inheritance-mode-vs" key="ValueSet-condition-inheritance-vs" name="Condition Inheritance Patterns"/>
<artifact id="ValueSet/dna-change-type-vs" key="ValueSet-dna-change-type" name="DNA Change Type"/>
<artifact id="StructureDefinition/diagnostic-implication" key="StructureDefinition-diagnostic-implication" name="Diagnostic Implication"/>
<artifact deprecated="true" key="DiagnosticReport" name="DiagnosticReport"/>
<artifact id="Observation/AnnotationExample" key="Observation-AnnotationExample" name="Example - ACMG Screening result"/>
<artifact id="Specimen/specimen-hla-r4" key="Specimen-specimen-hla-r4" name="Example - Buccal swab for HLA typing"/>
<artifact id="DiagnosticReport/report-CYP2C19" key="DiagnosticReport-report-CYP2C19" name="Example - CYP2C19 report from 1000 Genomes"/>
<artifact id="Bundle/compound-heterozygote" key="Bundle-compound-heterozygote" name="Example - Complex Variant (HGVS)"/>
<artifact id="Bundle/complexVariant-nonHGVS" key="Bundle-complexVariant-nonHGVS" name="Example - Complex Variant (unpacked)"/>
<artifact id="DiagnosticReport/PGxGenomicsReportEMERGE" key="DiagnosticReport-PGxGenomicsReportEMERGE" name="Example - DiagnosticReport-PGxGenomicsReportEMERGE"/>
<artifact id="Bundle/CG-IG-HLA-FullBundle-01" key="Bundle-CG-IG-HLA-FullBundle-01" name="Example - Full Bundle HLA genotyping for HLA-A, HLA-B, and HLA-C, using GLStrings"/>
<artifact id="Bundle/oncologyexamples-r4" key="Bundle-oncologyexamples-r4" name="Example - Full Bundle Oncology Example"/>
<artifact id="Bundle/diagnosticreport-cgexample" key="Bundle-diagnosticreport-cgexample" name="Example - Genomics Reporting"/>
<artifact id="DiagnosticReport/GenomicsReportExample01" key="DiagnosticReport-GenomicsReportExample01" name="Example - GenomicsReport"/>
<artifact id="Observation/GenotypeExample1" key="Observation-GenotypeExample1" name="Example - Genotype"/>
<artifact id="DiagnosticReport/diagnosticreport-hla-glstring-r4" key="DiagnosticReport-diagnosticreport-hla-glstring-r4" name="Example - HLA genotyping for HLA-A, HLA-B, and HLA-C, using GLStrings"/>
<artifact id="Observation/genotype-hla-a-glstring-r4" key="Observation-genotype-hla-a-glstring-r4" name="Example - HLA genotyping for HLA-A, using GLStrings"/>
<artifact id="Observation/obs-idh-ex" key="Observation-obs-idh-ex" name="Example - Inherited Disease Pathogenicity"/>
<artifact id="Observation/MicrosatelliteInstabilityExample01" key="Observation-MicrosatelliteInstabilityExample01" name="Example - MSI"/>
<artifact id="Task/MedicationRecommendationExample1" key="Task-MedicationRecommendationExample1" name="Example - MedicationRecommendation"/>
<artifact id="Bundle/oncology-diagnostic" key="Bundle-oncology-diagnostic" name="Example - Melanoma implication"/>
<artifact id="Bundle/oncology-report-example" key="Bundle-oncology-report-example" name="Example - Multiple Oncology Variant Report Example"/>
<artifact id="Observation/SNVexample" key="Observation-SNVexample" name="Example - NGS"/>
<artifact id="Observation/Pgx-geno-1001" key="Observation-Pgx-geno-1001" name="Example - Observation PGx Genotype 1"/>
<artifact id="Observation/Pgx-geno-1002" key="Observation-Pgx-geno-1002" name="Example - Observation PGx Genotype 2"/>
<artifact id="Observation/Pgx-geno-1003" key="Observation-Pgx-geno-1003" name="Example - Observation PGx Genotype 3"/>
<artifact id="Observation/OverallInterpExample2" key="Observation-OverallInterpExample2" name="Example - Observation PGx interpretation"/>
<artifact id="Observation/haplotype-hla-a-1-r4" key="Observation-haplotype-hla-a-1-r4" name="Example - Observation for a single HLA-A allele"/>
<artifact id="Observation/GrouperEx01" key="Observation-GrouperEx01" name="Example - Observation-GrouperEx01"/>
<artifact id="Observation/GrouperEx02" key="Observation-GrouperEx02" name="Example - Observation-GrouperEx02"/>
<artifact id="Observation/GrouperEx03" key="Observation-GrouperEx03" name="Example - Observation-GrouperEx03"/>
<artifact id="Observation/Pgx-var-1011" key="Observation-Pgx-var-1011" name="Example - Observation-Pgx-var-1011"/>
<artifact id="Observation/Pgx-var-1012" key="Observation-Pgx-var-1012" name="Example - Observation-Pgx-var-1012"/>
<artifact id="Observation/Pgx-var-1013" key="Observation-Pgx-var-1013" name="Example - Observation-Pgx-var-1013"/>
<artifact id="Observation/Pgx-var-1014" key="Observation-Pgx-var-1014" name="Example - Observation-Pgx-var-1014"/>
<artifact id="Observation/Pgx-var-1015" key="Observation-Pgx-var-1015" name="Example - Observation-Pgx-var-1015"/>
<artifact id="Observation/Pgx-var-1016" key="Observation-Pgx-var-1016" name="Example - Observation-Pgx-var-1016"/>
<artifact id="Observation/Pgx-var-1017" key="Observation-Pgx-var-1017" name="Example - Observation-Pgx-var-1017"/>
<artifact id="Observation/Pgx-var-1018" key="Observation-Pgx-var-1018" name="Example - Observation-Pgx-var-1018"/>
<artifact id="Observation/Pgx-var-1019" key="Observation-Pgx-var-1019" name="Example - Observation-Pgx-var-1019"/>
<artifact id="Observation/Pgx-var-1020" key="Observation-Pgx-var-1020" name="Example - Observation-Pgx-var-1020"/>
<artifact id="Observation/Pgx-var-1021" key="Observation-Pgx-var-1021" name="Example - Observation-Pgx-var-1021"/>
<artifact id="Observation/RegionStudiedPGx1" key="Observation-RegionStudiedPGx1" name="Example - Observation-RegionStudiedPGx1"/>
<artifact id="Observation/RegionStudiedPGx2" key="Observation-RegionStudiedPGx2" name="Example - Observation-RegionStudiedPGx2"/>
<artifact id="Observation/RegionStudiedPGx3" key="Observation-RegionStudiedPGx3" name="Example - Observation-RegionStudiedPGx3"/>
<artifact id="Observation/TxImp01" key="Observation-TxImp01" name="Example - Observation-TxImp01"/>
<artifact id="Observation/TxImp02" key="Observation-TxImp02" name="Example - Observation-TxImp02"/>
<artifact id="Observation/TxImp03" key="Observation-TxImp03" name="Example - Observation-TxImp03"/>
<artifact id="Observation/TxImp04" key="Observation-TxImp04" name="Example - Observation-TxImp04"/>
<artifact id="Observation/TxImp05" key="Observation-TxImp05" name="Example - Observation-TxImp05"/>
<artifact id="Observation/TxImp06" key="Observation-TxImp06" name="Example - Observation-TxImp06"/>
<artifact id="Observation/OverallInterpExample1" key="Observation-OverallInterpExample1" name="Example - Overall Interpretation"/>
<artifact id="Patient/CGPatientExample01" key="Patient-CGPatientExample01" name="Example - Patient"/>
<artifact id="Bundle/diagnosticreport-pgxexample" key="Bundle-diagnosticreport-pgxexample" name="Example - Pharmacogenomics"/>
<artifact id="Observation/SequencePhaseRelationExample1" key="Observation-SequencePhaseRelationExample1" name="Example - Sequence Phase Relation"/>
<artifact id="ServiceRequest/GenomicsServiceRequestExample01" key="ServiceRequest-GenomicsServiceRequestExample01" name="Example - Service Request"/>
<artifact id="ServiceRequest/servicerequest-hla-a-r4" key="ServiceRequest-servicerequest-hla-a-r4" name="Example - Service request for high-resolution HLA-A genotyping"/>
<artifact id="ServiceRequest/eMERGEServiceRequest" key="ServiceRequest-eMERGEServiceRequest" name="Example - ServiceRequest-eMERGEServiceRequest"/>
<artifact id="Specimen/GenomicSpecimenExample01" key="Specimen-GenomicSpecimenExample01" name="Example - Specimen"/>
<artifact id="Observation/TumorMutationBurdenExample01" key="Observation-TumorMutationBurdenExample01" name="Example - TMB"/>
<artifact deprecated="true" id="Task/TaskMedChgExample1" key="Task-TaskMedChgExample1" name="Example - TaskMedChg"/>
<artifact id="Observation/TherapeuticImplicationExample1" key="Observation-TherapeuticImplicationExample1" name="Example - TherapeuticImplication"/>
<artifact id="Observation/VariantExample1" key="Observation-VariantExample1" name="Example - Variant1"/>
<artifact id="Observation/VariantExample2" key="Observation-VariantExample2" name="Example - Variant2"/>
<artifact id="DiagnosticReport/sequence-phase-relation-CYP2C19" key="DiagnosticReport-sequence-phase-relation-CYP2C19" name="Example - subset of CYP2C19 report from 1000 Genomes showing phase"/>
<artifact id="Organization/ExampleOrg" key="Organization-ExampleOrg" name="Example Org"/>
<artifact id="Task/PGxRecEx01" key="Task-PGxRecEx01" name="Example Task - PGxRecEx01"/>
<artifact id="Task/PGxRecEx02" key="Task-PGxRecEx02" name="Example Task - PGxRecEx02"/>
<artifact id="Task/PGxRecEx03" key="Task-PGxRecEx03" name="Example Task - PGxRecEx03"/>
<artifact id="Task/PGxRecEx04" key="Task-PGxRecEx04" name="Example Task - PGxRecEx04"/>
<artifact id="Task/PGxRecEx05" key="Task-PGxRecEx05" name="Example Task - PGxRecEx05"/>
<artifact id="ValueSet/functional-effect-vs" key="ValueSet-functional-effect" name="Functional Effect"/>
<artifact id="StructureDefinition/finding" key="StructureDefinition-finding" name="Genomic Finding"/>
<artifact id="StructureDefinition/implication" key="StructureDefinition-implication" name="Genomic Implication"/>
<artifact id="StructureDefinition/genomics-artifact" key="StructureDefinition-genomics-artifact" name="Genomics Artifact"/>
<artifact id="StructureDefinition/genomics-base" key="StructureDefinition-genomics-base" name="Genomics Base"/>
<artifact id="StructureDefinition/genomics-report" key="StructureDefinition-genomics-report" name="Genomics Report"/>
<artifact id="StructureDefinition/genomics-report-risk" key="StructureDefinition-genomics-report-risk" name="Genomics Report Risk Assessment"/>
<artifact id="StructureDefinition/genotype" key="StructureDefinition-genotype" name="Genotype"/>
<artifact id="StructureDefinition/grouper" key="StructureDefinition-grouper" name="Grouper"/>
<artifact id="ValueSet/hgnc-vs" key="ValueSet-hgnc" name="HGNC Value Set"/>
<artifact id="ValueSet/hgvs-vs" key="ValueSet-hgvs" name="HGVS Value Set"/>
<artifact id="StructureDefinition/haplotype" key="StructureDefinition-haplotype" name="Haplotype"/>
<artifact id="ValueSet/high-low-codes-vs" key="ValueSet-high-low-codes" name="High/Low codes"/>
<artifact deprecated="true" key="ImplementationGuide" name="ImplementationGuide"/>
<artifact id="StructureDefinition/medication-recommendation" key="StructureDefinition-task-med-chg" name="Medication Usage Task"/>
<artifact id="StructureDefinition/msi" key="StructureDefinition-msi" name="Microsatellite instability"/>
<artifact id="ValueSet/molecular-consequence-vs" key="ValueSet-molecular-consequence" name="Molecular Consequence"/>
<artifact deprecated="true" key="Sequence" name="MolecularSequence"/>
<artifact deprecated="true" key="Observation" name="Observation"/>
<artifact id="OperationDefinition/find-subject-variants" key="OperationDefinition-find-subject-variants" name="Operation: $find-subject-variants"/>
<artifact id="StructureDefinition/overall-interpretation" key="StructureDefinition-overall-interpretation" name="Overall Interpretation"/>
<artifact id="StructureDefinition/recommended-action" key="StructureDefinition-RecommendedAction" name="Recommended Action"/>
<artifact id="StructureDefinition/followup-recommendation" key="StructureDefinition-task-rec-followup" name="Recommended Followup"/>
<artifact id="StructureDefinition/region-studied" key="StructureDefinition-region-studied" name="Region Studied"/>
<artifact deprecated="true" id="StructureDefinition/CGRelatedArtifact" key="StructureDefinition-CGRelatedArtifact" name="Related Artifact"/>
<artifact id="StructureDefinition/servicerequest" key="StructureDefinition-servicerequest" name="Request for Genomics Test"/>
<artifact deprecated="true" id="StructureDefinition/diagnosticReport-risk" key="StructureDefinition-diagnosticReport-risk" name="Risk Assessment Reference"/>
<artifact id="StructureDefinition/sequence-phase-relationship" key="StructureDefinition-sequence-phase-relationship" name="Sequence Phase Relationship"/>
<artifact id="CodeSystem/sequence-phase-relationship-cs" key="CodeSystem-SequencePhaseRelationshipCS" name="Sequence Phase Relationship Codes"/>
<artifact id="ValueSet/sequence-phase-relationship-vs" key="ValueSet-seq-phase-relationship" name="Sequence Phase Relationships"/>
<artifact id="StructureDefinition/specimen" key="StructureDefinition-specimen" name="Specimen"/>
<artifact id="StructureDefinition/supporting-information" key="StructureDefinition-SupportingInfo" name="Supporting Information"/>
<artifact id="CodeSystem/tbd-codes-cs" key="CodeSystem-TbdCodes" name="TBD Code System"/>
<artifact id="ValueSet/tbd-codes-vs" key="ValueSet-tbd" name="TBD Value Set"/>
<artifact deprecated="true" key="Task" name="Task"/>
<artifact id="StructureDefinition/therapeutic-implication" key="StructureDefinition-therapeutic-implication" name="Therapeutic Implication"/>
<artifact id="StructureDefinition/tmb" key="StructureDefinition-tmb" name="Tumor mutation burden"/>
<artifact id="StructureDefinition/variant" key="StructureDefinition-variant" name="Variant"/>
<artifact id="ValueSet/variant-inheritance-vs" key="ValueSet-variant-inheritance" name="Variant Inheritance"/>
<page key="NA" name="(NA)"/>
<page key="many" name="(many)"/>
<page deprecated="true" key="profiles" name="(profiles)"/>
<page key="v2" name="Appendix A: Relation to v2 reporting"/>
<page key="cgapps" name="Appendix B: Clinical Genomic Apps"/>
<page key="domain" name="Appendix C: HL7 Domain Analysis Model"/>
<page key="usecases" name="Appendix D: Query Guidance"/>
<page key="codings" name="Appendix E: External Coding Systems"/>
<page key="conversion" name="Appendix F: Conversion from STU3 Extensions"/>
<page key="molecularSequence" name="Appendix G: Molecular Sequence"/>
<page key="Glossary" name="Appendix H: Glossary"/>
<page key="artifacts" name="Artifact List"/>
<page key="general" name="General Genomic Reporting"/>
<page key="background" name="Genomics Background"/>
<page key="histocompatibility" name="Histocompatibility and Immunogenetics Reporting"/>
<page key="index" name="Home"/>
<page key="operations" name="Operations"/>
<page key="pharmacogenomics" name="Pharmacogenomic Reporting"/>
<page key="somatics" name="Somatic Reporting"/>
<page key="toc" name="Table of Contents"/>
<page key="downloads" name="Useful Downloads"/>
<page key="sequencing" name="Variant Reporting"/>
<page deprecated="true" key="documentation" name="documentation"/>
<page deprecated="true" key="genomics" name="genomics"/>
</specification>