Genomics Reporting Implementation Guide
3.0.0-ballot - Ballot International flag

This page is part of the Genetic Reporting Implementation Guide (v3.0.0-ballot: STU 3 Ballot 1) based on FHIR (HL7® FHIR® Standard) R4. The current version which supersedes this version is 3.0.0. 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 Population Diagnostic Implications
.... 19.2 Find Population Molecular Consequences
.... 19.3 Find Population Specific Haplotypes
.... 19.4 Find Population Specific Variants
.... 19.5 Find Population Structural Intersecting Variants
.... 19.6 Find Population Structural Subsuming Variants
.... 19.7 Find Population Treatment Implications
.... 19.8 Find Study Metadata
.... 19.9 Find Subject Diagnostic Implications
.... 19.10 Find Subject Haplotypes
.... 19.11 Find Subject Molecular Consequences
.... 19.12 Find Subject Specific Haplotypes
.... 19.13 Find Subject Specific Variants
.... 19.14 Find Subject Structural Intersecting Variants
.... 19.15 Find Subject Structural Subsuming Variants
.... 19.16 Find Subject Treatment Implications
.... 19.17 Find Subject Variants
.... 19.18 Genomic Base
.... 19.19 Genomic Finding
.... 19.20 Genomic Implication
.... 19.21 Diagnostic Implication
.... 19.22 Followup Recommendation
.... 19.23 Genomic Data File
.... 19.24 Genomic Report
.... 19.25 Genomic Study
.... 19.26 Genomic Study Analysis
.... 19.27 Genotype
.... 19.28 Haplotype
.... 19.29 Medication Recommendation
.... 19.30 Molecular Biomarker
.... 19.31 Molecular Consequence
.... 19.32 Overall Interpretation
.... 19.33 Sequence Phase Relationship
.... 19.34 Therapeutic Implication
.... 19.35 Variant
.... 19.36 Coded Annotation
.... 19.37 Annotation Code
.... 19.38 Genomic Report Note
.... 19.39 Genomic Risk Assessment
.... 19.40 Genomic Study Analysis Change Type
.... 19.41 Genomic Study Analysis Device
.... 19.42 Genomic Study Analysis Extension
.... 19.43 Genomic Study Analysis Focus
.... 19.44 Genomic Study Analysis Genome Build
.... 19.45 Genomic Study Analysis Input
.... 19.46 Genomic Study Analysis Method Type
.... 19.47 Genomic Study Analysis Metrics
.... 19.48 Genomic Study Analysis Output
.... 19.49 Genomic Study Analysis Protocol Performed
.... 19.50 Genomic Study Analysis Regions
.... 19.51 Genomic Study Analysis Specimen
.... 19.52 Genomic Study Analysis Title
.... 19.53 Genomic Study Reference
.... 19.54 Genomic Study Referrer Extension
.... 19.55 Medication Assessed reference to a FHIR resource
.... 19.56 Recommended Action
.... 19.57 Related Artifact for Observation component
.... 19.58 Repeat Motif Order
.... 19.59 Therapy Assessed reference to a FHIR resource
.... 19.60 Coded Annotation Types
.... 19.61 Condition Inheritance Patterns
.... 19.62 DNA Change Type
.... 19.63 Evidence Level Examples
.... 19.64 Functional Effect Value Set
.... 19.65 Genetic Therapeutic Implications
.... 19.66 Genomic Study Change Type ValueSet
.... 19.67 Genomic Study Data Format ValueSet
.... 19.68 Genomic Study Method Type ValueSet
.... 19.69 Genomic Study Status ValueSet
.... 19.70 Genomic Study Type ValueSet
.... 19.71 High Low codes
.... 19.72 HUGO Gene Nomenclature Committee Gene Names (HGNC)
.... 19.73 Human Genome Variation Society (HGVS) Nomenclature
.... 19.74 Molecular Biomarker Categories
.... 19.75 Molecular Biomarker Codes
.... 19.76 Molecular Consequence Value Set
.... 19.77 Sequence Phase Relationships
.... 19.78 To Be Determined Value Set
.... 19.79 Variant Confidence Status
.... 19.80 ClinVar Evidence Level Example Codes
.... 19.81 Coded Annotation Type Codes
.... 19.82 Genomic Study Change Type CodeSystem
.... 19.83 Genomic Study Data Format CodeSystem
.... 19.84 Genomic Study Method Type CodeSystem
.... 19.85 Genomic Study Status CodeSystem
.... 19.86 Genomic Study Type CodeSystem
.... 19.87 Molecular Biomarker Ontology Codes
.... 19.88 PharmGKB Evidence Level Example Codes
.... 19.89 Sequence Phase Relationship Codes
.... 19.90 To Be Determined Codes
.... 19.91 Variant Confidence Status Codes
.... 19.92 DNA Change Type Map
.... 19.93 Genomic Study Status Map
.... 19.94 analysisTumorNormalDNA
.... 19.95 analysisTumorRNA
.... 19.96 AnnotationExample
.... 19.97 ATR-insertion-molc
.... 19.98 ATR-insertion-significance
.... 19.99 ATR-insertion-var
.... 19.100 bundle-CG-IG-HLA-FullBundle-01
.... 19.101 bundle-cgexample
.... 19.102 bundle-cgexample-withGrouping
.... 19.103 bundle-complexVariant-nonHGVS
.... 19.104 bundle-compound-heterozygote
.... 19.105 bundle-CYP2C19
.... 19.106 bundle-oncology-diagnostic
.... 19.107 bundle-oncology-report-example
.... 19.108 bundle-oncologyexamples-r4
.... 19.109 bundle-oncologyexamples-r4-withGrouping
.... 19.110 bundle-pgxexample
.... 19.111 bundle-sequence-phase-relation-CYP2C19
.... 19.112 CGPatientExample01
.... 19.113 CNVAnalysis-called
.... 19.114 denovoChild
.... 19.115 denovoFather
.... 19.116 denovoMother
.... 19.117 diagnosticreport-hla-glstring-r4
.... 19.118 EGFR-L858R-molc
.... 19.119 EGFR-L858R-significance
.... 19.120 EGFR-L858R-therapuDrug1
.... 19.121 EGFR-L858R-therapuDrug2
.... 19.122 EGFR-L858R-var
.... 19.123 eMERGEServiceRequest
.... 19.124 ExampleGermlineCNV
.... 19.125 ExampleGermlineDEL
.... 19.126 ExampleGermlineINV
.... 19.127 ExampleLab
.... 19.128 ExampleOrg
.... 19.129 ExamplePatient
.... 19.130 ExampleServiceRequest
.... 19.131 ExampleSomaticCNV
.... 19.132 ExampleSomaticDEL
.... 19.133 ExampleSomaticINV
.... 19.134 ExampleSpecimen
.... 19.135 FindALLPopulationSpecificVariantsOutput
.... 19.136 FindANYPopulationSpecificVariantsOutput
.... 19.137 FindPopulationDxImplicationsOutput
.... 19.138 FindPopulationMolecConseqOutput
.... 19.139 FindPopulationSpecificHaplotypesOutput
.... 19.140 FindPopulationStructuralIntersectingVariantsOutput
.... 19.141 FindPopulationStructuralSubsumingVariantsOutput
.... 19.142 FindPopulationTxImplicationsOutput
.... 19.143 FindStudyMetadataOutput
.... 19.144 FindSubjectDxImplicationsOutput
.... 19.145 FindSubjectHaplotypesOutput
.... 19.146 FindSubjectMolecConseqOutput
.... 19.147 FindSubjectSpecificHaplotypesOutput
.... 19.148 FindSubjectSpecificVariantsOutput
.... 19.149 FindSubjectStructuralIntersectingVariantsOutput
.... 19.150 FindSubjectStructuralSubsumingVariantsOutput
.... 19.151 FindSubjectTxImplicationsOutput
.... 19.152 FindSubjectVariantsOutput
.... 19.153 FullGenome-GRCh38
.... 19.154 genomicFileFatherBAM
.... 19.155 genomicFileMotherBAM
.... 19.156 genomicFileProbandBAM
.... 19.157 genomicFileProbandVCF
.... 19.158 genomicPatient
.... 19.159 GenomicReportExample01
.... 19.160 genomicServiceRequest
.... 19.161 GenomicServiceRequestExample01
.... 19.162 genomicSpecimen
.... 19.163 GenomicSpecimenExample01
.... 19.164 GenomicSpecimenExample02
.... 19.165 genomicstudy-trio2
.... 19.166 genomicstudyanalysis-trio2
.... 19.167 genomicVCFfile-cnv
.... 19.168 genomicVCFfile-simple
.... 19.169 Genotype-Clinical-Trial-Example-using-haplotypes
.... 19.170 genotype-hla-a-glstring-r4
.... 19.171 GenotypeExample1
.... 19.172 GenotypeExamplePharmVar
.... 19.173 GenRiskDiabetesT2
.... 19.174 GrouperEx01
.... 19.175 GrouperEx02
.... 19.176 GrouperEx03
.... 19.177 haplotype-hla-a-1-r4
.... 19.178 HaplotypeExamplePharmVar01
.... 19.179 HaplotypeExamplePharmVar02
.... 19.180 HaplotypeSet-Clinical-Trial-Example-1of2
.... 19.181 HaplotypeSet-Clinical-Trial-Example-2of2
.... 19.182 HER2byImmuneStainExample
.... 19.183 HER2byImmunoassayExample
.... 19.184 HG00403
.... 19.185 HLA-A-haplotype1
.... 19.186 HLA-A-haplotype2
.... 19.187 HLA-B-haplotype1
.... 19.188 HLA-B-haplotype2
.... 19.189 HLA-C-haplotype1
.... 19.190 HLA-C-haplotype2
.... 19.191 ISCN-CMLExample
.... 19.192 ISCN-CMLImplication
.... 19.193 ISCN-NormalExample
.... 19.194 lungMass
.... 19.195 lungMass-analysis1
.... 19.196 lungMass-analysis2
.... 19.197 MedicationRecommendationExample1
.... 19.198 MedicationStatementWarfarin
.... 19.199 MicrosatelliteInstabilityExample01
.... 19.200 molec-conseq1
.... 19.201 molec-conseq2
.... 19.202 molec-conseq3
.... 19.203 molec-conseq4
.... 19.204 MSH2-del-disease
.... 19.205 MSH2-del-molc
.... 19.206 MSH2-del-var
.... 19.207 MSIExample
.... 19.208 MultipleRepeatExpansions
.... 19.209 normalSpecimen
.... 19.210 NOTCH1-significance
.... 19.211 NOTCH1-uncertain-molc
.... 19.212 NOTCH1-uncertain-var
.... 19.213 NTHL1-snv-disease
.... 19.214 NTHL1-snv-molc
.... 19.215 NTHL1-snv-var
.... 19.216 obs-idh-ex
.... 19.217 orderingPractitioner
.... 19.218 overallInt
.... 19.219 OverallInterpExample1
.... 19.220 OverallInterpExample2
.... 19.221 pathologistPractitioner
.... 19.222 PDL1Example
.... 19.223 performingOrganization
.... 19.224 Pgx-geno-1001
.... 19.225 Pgx-geno-1002
.... 19.226 Pgx-geno-1003
.... 19.227 Pgx-var-1011
.... 19.228 Pgx-var-1012
.... 19.229 Pgx-var-1013
.... 19.230 Pgx-var-1014
.... 19.231 Pgx-var-1015
.... 19.232 Pgx-var-1016
.... 19.233 Pgx-var-1017
.... 19.234 Pgx-var-1018
.... 19.235 Pgx-var-1019
.... 19.236 Pgx-var-1020
.... 19.237 Pgx-var-1021
.... 19.238 PGxGenomicReportEMERGE
.... 19.239 PGxGenomicReportEMERGE-withGrouping
.... 19.240 PGXGenomicStudy
.... 19.241 PGXGenomicStudyAnalysis
.... 19.242 PGxRecEx01
.... 19.243 PGxRecEx02
.... 19.244 PGxRecEx03
.... 19.245 PGxRecEx04
.... 19.246 PGxRecEx05
.... 19.247 PolyGenicDiagnosticImpExample
.... 19.248 practitioner02
.... 19.249 RepeatExpansion
.... 19.250 ROS1-Fusion
.... 19.251 ROS1-Fusion-disease
.... 19.252 ROS1-Fusion-therapuDrug
.... 19.253 ROS1-Fusion-therapuTrial
.... 19.254 ROS1-Fusion-var
.... 19.255 SequencePhaseRelationExample1
.... 19.256 SequencingProcedure
.... 19.257 servicerequest-hla-a-r4
.... 19.258 SimpleVariantAnalysis-called
.... 19.259 SNVexample
.... 19.260 somaticPatient
.... 19.261 somaticReport
.... 19.262 somaticServiceRequest
.... 19.263 somaticStudy
.... 19.264 somaticVCFfile
.... 19.265 specimen-hla-r4
.... 19.266 STAG2-insertion-molc
.... 19.267 STAG2-insertion-significance
.... 19.268 STAG2-insertion-var
.... 19.269 supervisorPractitioner
.... 19.270 Therapeutic-Implication-Clinical-Trial-2
.... 19.271 Therapeutic-Implication-Clinical-Trial-Somatic
.... 19.272 TherapeuticImplicationExample1
.... 19.273 TMB-therapuDrug
.... 19.274 TMBExample
.... 19.275 triodenovo-software
.... 19.276 TumorMutationBurdenExample01
.... 19.277 tumorSpecimen
.... 19.278 TxImp01
.... 19.279 TxImp02
.... 19.280 TxImp03
.... 19.281 TxImp04
.... 19.282 TxImp05
.... 19.283 TxImp06
.... 19.284 UncallableRegions
.... 19.285 Variant-Somatic-Clinical-Trial
.... 19.286 variant-with-molec-consequences
.... 19.287 VariantExample
.... 19.288 VariantExample1
.... 19.289 VariantExample2
.... 19.290 WES-FullSequencedRegion-GRCh38
.... 19.291 WES-UncallableRegions-GRCh38
.... 19.292 ZFHX3-significance
.... 19.293 ZFHX3-uncertain-molc
.... 19.294 ZFHX3-uncertain-var