Genomics Reporting Implementation Guide
2.0.0 - trial-use

This page is part of the Genetic Reporting Implementation Guide (v2.0.0: STU 2) based on FHIR R4. This is the current published version in its permanent home (it will always be available at this URL). For a full list of available versions, see the Directory of published versions

Table of Contents

..0 Table of Contents
...1 Home Page
...2 Genomics Background
...3 General Genomic Reporting
...4 Variant Reporting
...5 Pharmacogenomic Reporting
...6 Somatic Reporting
...7 Histocompatibility and Immunogenetics Reporting
...8 Operations
...9 Useful Downloads
...10 Appendix A: Relation to v2 reporting
...11 Appendix B: Clinical Genomic Apps
...12 Appendix C: HL7 Domain Analysis Model
...13 Appendix D: Query Guidance
...14 Appendix E: External Coding Systems
...15 Appendix F: Conversion from STU3 Extensions
...16 Appendix G: Molecular Sequence
...17 Appendix H: Grouping Guidance
...18 Appendix I: Glossary
...19 Artifacts Summary
....19.1 Find Subject Variants
....19.2 Genomics Finding
....19.3 Genomics Implication
....19.4 Genomics Base
....19.5 Diagnostic Implication
....19.6 Followup Recommendation
....19.7 Genomics DocumentReference
....19.8 Genomics Report
....19.9 Genotype
....19.10 Haplotype
....19.11 Microsatellite Instability
....19.12 Medication Recommendation
....19.13 Overall Interpretation
....19.14 Region Studied
....19.15 Sequence Phase Relationship
....19.16 Tumor Mutation Burden
....19.17 Therapeutic Implication
....19.18 Variant
....19.19 Coded Annotation
....19.20 Annotation Code
....19.21 Genomic Report Note
....19.22 Genomics Artifact
....19.23 Genomics File
....19.24 Genomics Risk Assessment
....19.25 Medication Assessed
....19.26 Recommended Action
....19.27 Therapy Assessed
....19.28 Coded Annotation Types
....19.29 Condition Inheritance Patterns
....19.30 DNA Change Type
....19.31 Evidence Level Examples
....19.32 Functional Effect
....19.33 Genetic Therapeutic Implications
....19.34 HUGO Gene Nomenclature Committee Gene Names (HGNC)
....19.35 Human Genome Variation Society (HGVS) Nomenclature
....19.36 High Low codes
....19.37 Molecular Consequence
....19.38 Sequence Phase Relationships
....19.39 To Be Determined Value Set
....19.40 Variant Confidence Status
....19.41 Variant Inheritances
....19.42 ClinVar Evidence Level Example Codes
....19.43 Coded Annotation Type Codes
....19.44 PharmGKB Evidence Level Example Codes
....19.45 Sequence Phase Relationship Codes
....19.46 To Be Determined Codes
....19.47 Variant Confidence Status Codes
....19.48 DNA Change Type Map
....19.49 AnnotationExample
....19.50 CGPatientExample01
....19.51 ExampleGermlineCNV
....19.52 ExampleGermlineDEL
....19.53 ExampleGermlineINV
....19.54 ExampleLab
....19.55 ExampleOrg
....19.56 ExamplePatient
....19.57 ExampleServiceRequest
....19.58 ExampleSomaticCNV
....19.59 ExampleSomaticDEL
....19.60 ExampleSomaticINV
....19.61 ExampleSpecimen
....19.62 GenRiskDiabetesT2
....19.63 GenomicSpecimenExample01
....19.64 GenomicSpecimenExample02
....19.65 GenomicsReportExample01
....19.66 GenomicsServiceRequestExample01
....19.67 Genotype-Clinical-Trial-Example-using-haplotypes
....19.68 GenotypeExample1
....19.69 GenotypeExamplePharmVar
....19.70 GrouperEx01
....19.71 GrouperEx02
....19.72 GrouperEx03
....19.73 HaplotypeExamplePharmVar01
....19.74 HaplotypeExamplePharmVar02
....19.75 HaplotypeSet-Clinical-Trial-Example-1of2
....19.76 HaplotypeSet-Clinical-Trial-Example-2of2
....19.77 MedicationRecommendationExample1
....19.78 MedicationStatementWarfarin
....19.79 MicrosatelliteInstabilityExample01
....19.80 OverallInterpExample1
....19.81 OverallInterpExample2
....19.82 PGxGenomicsReportEMERGE
....19.83 PGxGenomicsReportEMERGE-withGrouping
....19.84 PGxRecEx01
....19.85 PGxRecEx02
....19.86 PGxRecEx03
....19.87 PGxRecEx04
....19.88 PGxRecEx05
....19.89 Pgx-geno-1001
....19.90 Pgx-geno-1002
....19.91 Pgx-geno-1003
....19.92 Pgx-var-1011
....19.93 Pgx-var-1012
....19.94 Pgx-var-1013
....19.95 Pgx-var-1014
....19.96 Pgx-var-1015
....19.97 Pgx-var-1016
....19.98 Pgx-var-1017
....19.99 Pgx-var-1018
....19.100 Pgx-var-1019
....19.101 Pgx-var-1020
....19.102 Pgx-var-1021
....19.103 PolyGenicDiagnosticImpExample
....19.104 RegionStudiedPGx1
....19.105 RegionStudiedPGx2
....19.106 RegionStudiedPGx3
....19.107 SNVexample
....19.108 SequencePhaseRelationExample1
....19.109 Therapeutic-Implication-Clinical-Trial-2
....19.110 Therapeutic-Implication-Clinical-Trial-Somatic
....19.111 TherapeuticImplicationExample1
....19.112 TumorMutationBurdenExample01
....19.113 TxImp01
....19.114 TxImp02
....19.115 TxImp03
....19.116 TxImp04
....19.117 TxImp05
....19.118 TxImp06
....19.119 VCFFile
....19.120 Variant-Somatic-Clinical-Trial
....19.121 VariantExample1
....19.122 VariantExample2
....19.123 bundle-CG-IG-HLA-FullBundle-01
....19.124 bundle-CYP2C19
....19.125 bundle-cgexample
....19.126 bundle-cgexample-withGrouping
....19.127 bundle-complexVariant-nonHGVS
....19.128 bundle-compound-heterozygote
....19.129 bundle-oncology-diagnostic
....19.130 bundle-oncology-report-example
....19.131 bundle-oncologyexamples-r4
....19.132 bundle-oncologyexamples-r4-withGrouping
....19.133 bundle-pgxexample
....19.134 bundle-sequence-phase-relation-CYP2C19
....19.135 diagnosticreport-hla-glstring-r4
....19.136 eMERGEServiceRequest
....19.137 genotype-hla-a-glstring-r4
....19.138 haplotype-hla-a-1-r4
....19.139 obs-idh-ex
....19.140 servicerequest-hla-a-r4
....19.141 specimen-hla-r4