Genomics Reporting Implementation Guide
4.0.0-ballot - STU 4 ballot International flag

Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 4.0.0-ballot built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/genomics-reporting/ and changes regularly. See the Directory of published versions

Table of Contents

Page standards status: Informative
.. 0 Table of Contents
... 1 Home Page
... 2 Genomic Background
... 3 General Genomic Reporting
... 4 Variant Reporting
... 5 Pharmacogenomic Reporting
... 6 Somatic Reporting
... 7 Histocompatibility and Immunogenetic Reporting
... 8 Genomic 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 FHIR Core STU3
... 16 Appendix G: Molecular Sequence
... 17 Appendix H: Grouping Guidance
... 18 Appendix I: Glossary
... 19 Change Log
... 20 Artifacts Summary
.... 20.1 Find Population Diagnostic Implications
.... 20.2 Find Population Molecular Consequences
.... 20.3 Find Population Specific Haplotypes
.... 20.4 Find Population Specific Variants
.... 20.5 Find Population Structural Intersecting Variants
.... 20.6 Find Population Structural Subsuming Variants
.... 20.7 Find Population Treatment Implications
.... 20.8 Find Study Metadata
.... 20.9 Find Subject Diagnostic Implications
.... 20.10 Find Subject Haplotypes
.... 20.11 Find Subject Molecular Consequences
.... 20.12 Find Subject Specific Haplotypes
.... 20.13 Find Subject Specific Variants
.... 20.14 Find Subject Structural Intersecting Variants
.... 20.15 Find Subject Structural Subsuming Variants
.... 20.16 Find Subject Treatment Implications
.... 20.17 Find Subject Variants
.... 20.18 Genomic Base
.... 20.19 Genomic Finding
.... 20.20 Genomic Implication
.... 20.21 Diagnostic Implication
.... 20.22 Followup Recommendation
.... 20.23 Genomic Annotation
.... 20.24 Genomic Data File
.... 20.25 Genomic Report
.... 20.26 Genomic Study
.... 20.27 Genomic Study Analysis
.... 20.28 Genotype
.... 20.29 Haplotype
.... 20.30 Medication Recommendation
.... 20.31 Molecular Biomarker
.... 20.32 Molecular Consequence
.... 20.33 Sequence Phase Relationship
.... 20.34 Therapeutic Implication
.... 20.35 Variant
.... 20.36 Coded Annotation
.... 20.37 Annotation Code
.... 20.38 Genomic Report Note
.... 20.39 Genomic Risk Assessment
.... 20.40 Genomic Study Analysis Change Type
.... 20.41 Genomic Study Analysis Device
.... 20.42 Genomic Study Analysis Extension
.... 20.43 Genomic Study Analysis Focus
.... 20.44 Genomic Study Analysis Genome Build
.... 20.45 Genomic Study Analysis Input
.... 20.46 Genomic Study Analysis Method Type
.... 20.47 Genomic Study Analysis Metrics
.... 20.48 Genomic Study Analysis Output
.... 20.49 Genomic Study Analysis Protocol Performed
.... 20.50 Genomic Study Analysis Regions
.... 20.51 Genomic Study Analysis Source Class
.... 20.52 Genomic Study Analysis Specimen
.... 20.53 Genomic Study Analysis Title
.... 20.54 Genomic Study Reference
.... 20.55 Genomic Study Referrer Extension
.... 20.56 KnowledgebaseAncestryGroup
.... 20.57 Medication Assessed reference to a FHIR resource
.... 20.58 Recommended Action
.... 20.59 Related Artifact for Observation component
.... 20.60 Repeat Motif Order
.... 20.61 Therapy Assessed reference to a FHIR resource
.... 20.62 Coded Annotation Types
.... 20.63 Condition Inheritance Patterns
.... 20.64 DNA Change Type
.... 20.65 Evidence Level Examples
.... 20.66 Functional Effect Value Set
.... 20.67 Genetic Therapeutic Implications
.... 20.68 Genomic Study Change Type ValueSet
.... 20.69 Genomic Study Data Format ValueSet
.... 20.70 Genomic Study Method Type ValueSet
.... 20.71 Genomic Study Status ValueSet
.... 20.72 Genomic Study Type ValueSet
.... 20.73 HUGO Gene Nomenclature Committee Gene Names (HGNC)
.... 20.74 Human Genome Variation Society (HGVS) Nomenclature
.... 20.75 Knowledge Base Version Codes
.... 20.76 Molecular Biomarker Categories
.... 20.77 Molecular Biomarker Codes
.... 20.78 Molecular Consequence Value Set
.... 20.79 Sequence Phase Relationships
.... 20.80 To Be Determined Value Set
.... 20.81 Variant Confidence Status
.... 20.82 ClinVar Evidence Level Example Codes
.... 20.83 Coded Annotation Type Codes
.... 20.84 Genomic Study Change Type CodeSystem
.... 20.85 Genomic Study Data Format CodeSystem
.... 20.86 Genomic Study Method Type CodeSystem
.... 20.87 Genomic Study Status CodeSystem
.... 20.88 Genomic Study Type CodeSystem
.... 20.89 Knowledge Base Codes
.... 20.90 Molecular Biomarker Ontology Codes
.... 20.91 PharmGKB Evidence Level Example Codes
.... 20.92 Sequence Phase Relationship Codes
.... 20.93 To Be Determined Codes
.... 20.94 Variant Confidence Status Codes
.... 20.95 DNA Change Type Map
.... 20.96 Genomic Study Status Map
.... 20.97 analysisTumorNormalDNA
.... 20.98 analysisTumorRNA
.... 20.99 AnnotationExample
.... 20.100 ATR-insertion-molc
.... 20.101 ATR-insertion-significance
.... 20.102 ATR-insertion-var
.... 20.103 bundle-CG-IG-HLA-FullBundle-01
.... 20.104 bundle-cgexample
.... 20.105 bundle-cgexample-withGrouping
.... 20.106 bundle-complexVariant-nonHGVS
.... 20.107 bundle-compound-heterozygote
.... 20.108 bundle-CYP2C19
.... 20.109 bundle-oncology-diagnostic
.... 20.110 bundle-oncology-report-example
.... 20.111 bundle-oncologyexamples-r4
.... 20.112 bundle-oncologyexamples-r4-withGrouping
.... 20.113 bundle-pgxexample
.... 20.114 bundle-sequence-phase-relation-CYP2C19
.... 20.115 CGPatientExample01
.... 20.116 CNVAnalysis-called
.... 20.117 denovoChild
.... 20.118 denovoFather
.... 20.119 denovoMother
.... 20.120 diagnosticImplication-interact-smn1-smn2
.... 20.121 diagnosticreport-hla-glstring-r4
.... 20.122 EGFR-L858R-molc
.... 20.123 EGFR-L858R-significance
.... 20.124 EGFR-L858R-therapuDrug1
.... 20.125 EGFR-L858R-therapuDrug2
.... 20.126 EGFR-L858R-var
.... 20.127 eMERGEServiceRequest
.... 20.128 ExampleGermlineCNV
.... 20.129 ExampleGermlineDEL
.... 20.130 ExampleGermlineINV
.... 20.131 ExampleLab
.... 20.132 ExampleOrg
.... 20.133 ExamplePatient
.... 20.134 ExampleServiceRequest
.... 20.135 ExampleSomaticCNV
.... 20.136 ExampleSomaticDEL
.... 20.137 ExampleSomaticINV
.... 20.138 ExampleSpecimen
.... 20.139 FindALLPopulationSpecificVariantsOutput
.... 20.140 FindANYPopulationSpecificVariantsOutput
.... 20.141 FindPopulationDxImplicationsOutput
.... 20.142 FindPopulationMolecConseqOutput
.... 20.143 FindPopulationSpecificHaplotypesOutput
.... 20.144 FindPopulationStructuralIntersectingVariantsOutput
.... 20.145 FindPopulationStructuralSubsumingVariantsOutput
.... 20.146 FindPopulationTxImplicationsOutput
.... 20.147 FindStudyMetadataOutput
.... 20.148 FindSubjectDxImplicationsOutput
.... 20.149 FindSubjectHaplotypesOutput
.... 20.150 FindSubjectMolecConseqOutput
.... 20.151 FindSubjectSpecificHaplotypesOutput
.... 20.152 FindSubjectSpecificVariantsOutput
.... 20.153 FindSubjectStructuralIntersectingVariantsOutput
.... 20.154 FindSubjectStructuralSubsumingVariantsOutput
.... 20.155 FindSubjectTxImplicationsOutput
.... 20.156 FindSubjectVariantsOutput
.... 20.157 FullGenome-GRCh38
.... 20.158 genomicFileFatherBAM
.... 20.159 genomicFileMotherBAM
.... 20.160 genomicFileProbandBAM
.... 20.161 genomicFileProbandVCF
.... 20.162 genomicPatient
.... 20.163 GenomicReportExample01
.... 20.164 genomicServiceRequest
.... 20.165 GenomicServiceRequestExample01
.... 20.166 genomicSpecimen
.... 20.167 GenomicSpecimenExample01
.... 20.168 GenomicSpecimenExample02
.... 20.169 genomicstudy-trio2
.... 20.170 genomicstudyanalysis-trio2
.... 20.171 genomicVCFfile-cnv
.... 20.172 genomicVCFfile-simple
.... 20.173 Genotype-Clinical-Trial-Example-using-haplotypes
.... 20.174 genotype-hla-a-glstring-r4
.... 20.175 GenotypeExample1
.... 20.176 GenotypeExamplePharmVar
.... 20.177 GenRiskDiabetesT2
.... 20.178 GrouperEx01
.... 20.179 GrouperEx02
.... 20.180 GrouperEx03
.... 20.181 haplotype-hla-a-1-r4
.... 20.182 HaplotypeExamplePharmVar01
.... 20.183 HaplotypeExamplePharmVar02
.... 20.184 HaplotypeSet-Clinical-Trial-Example-1of2
.... 20.185 HaplotypeSet-Clinical-Trial-Example-2of2
.... 20.186 HER2byImmuneStainExample
.... 20.187 HER2byImmunoassayExample
.... 20.188 HG00403
.... 20.189 HLA-A-haplotype1
.... 20.190 HLA-A-haplotype2
.... 20.191 HLA-B-haplotype1
.... 20.192 HLA-B-haplotype2
.... 20.193 HLA-C-haplotype1
.... 20.194 HLA-C-haplotype2
.... 20.195 ISCN-CMLExample
.... 20.196 ISCN-CMLImplication
.... 20.197 ISCN-NormalExample
.... 20.198 lungMass
.... 20.199 lungMass-analysis1
.... 20.200 lungMass-analysis2
.... 20.201 MedicationRecommendationExample1
.... 20.202 MedicationStatementWarfarin
.... 20.203 MicrosatelliteInstabilityExample01
.... 20.204 molec-conseq1
.... 20.205 molec-conseq2
.... 20.206 molec-conseq3
.... 20.207 molec-conseq4
.... 20.208 MSH2-del-disease
.... 20.209 MSH2-del-molc
.... 20.210 MSH2-del-var
.... 20.211 MSIExample
.... 20.212 MultipleRepeatExpansions
.... 20.213 normalSpecimen
.... 20.214 NOTCH1-significance
.... 20.215 NOTCH1-uncertain-molc
.... 20.216 NOTCH1-uncertain-var
.... 20.217 NTHL1-snv-disease
.... 20.218 NTHL1-snv-molc
.... 20.219 NTHL1-snv-var
.... 20.220 obs-idh-ex
.... 20.221 obs1-interact-smn1-smn2
.... 20.222 obs2-interact-smn1-smn2
.... 20.223 orderingPractitioner
.... 20.224 pathologistPractitioner
.... 20.225 PDL1Example
.... 20.226 performingOrganization
.... 20.227 Pgx-geno-1001
.... 20.228 Pgx-geno-1002
.... 20.229 Pgx-geno-1003
.... 20.230 Pgx-var-1011
.... 20.231 Pgx-var-1012
.... 20.232 Pgx-var-1013
.... 20.233 Pgx-var-1014
.... 20.234 Pgx-var-1015
.... 20.235 Pgx-var-1016
.... 20.236 Pgx-var-1017
.... 20.237 Pgx-var-1018
.... 20.238 Pgx-var-1019
.... 20.239 Pgx-var-1020
.... 20.240 Pgx-var-1021
.... 20.241 PGxGenomicReportEMERGE
.... 20.242 PGxGenomicReportEMERGE-withGrouping
.... 20.243 PGXGenomicStudy
.... 20.244 PGXGenomicStudyAnalysis
.... 20.245 PGxRecEx01
.... 20.246 PGxRecEx02
.... 20.247 PGxRecEx03
.... 20.248 PGxRecEx04
.... 20.249 PGxRecEx05
.... 20.250 PolyGenicDiagnosticImpExample
.... 20.251 pop-allele-freq
.... 20.252 practitioner02
.... 20.253 RepeatExpansion
.... 20.254 ROS1-Fusion
.... 20.255 ROS1-Fusion-disease
.... 20.256 ROS1-Fusion-therapuDrug
.... 20.257 ROS1-Fusion-therapuTrial
.... 20.258 ROS1-Fusion-var
.... 20.259 SequencePhaseRelationExample1
.... 20.260 SequencingProcedure
.... 20.261 servicerequest-hla-a-r4
.... 20.262 SimpleVariantAnalysis-called
.... 20.263 SNVexample
.... 20.264 somaticPatient
.... 20.265 somaticReport
.... 20.266 somaticServiceRequest
.... 20.267 somaticStudy
.... 20.268 somaticVCFfile
.... 20.269 specimen-hla-r4
.... 20.270 STAG2-insertion-molc
.... 20.271 STAG2-insertion-significance
.... 20.272 STAG2-insertion-var
.... 20.273 supervisorPractitioner
.... 20.274 Therapeutic-Implication-Clinical-Trial-2
.... 20.275 Therapeutic-Implication-Clinical-Trial-Somatic
.... 20.276 TherapeuticImplicationExample1
.... 20.277 therapuDrug1-interact-smn1-smn2
.... 20.278 therapuDrug2-interact-smn1-smn2
.... 20.279 therapuDrug3-interact-smn1-smn2
.... 20.280 TMB-therapuDrug
.... 20.281 TMBExample
.... 20.282 triodenovo-software
.... 20.283 TumorMutationBurdenExample01
.... 20.284 tumorSpecimen
.... 20.285 TxImp01
.... 20.286 TxImp02
.... 20.287 TxImp03
.... 20.288 TxImp04
.... 20.289 TxImp05
.... 20.290 TxImp06
.... 20.291 UncallableRegions
.... 20.292 Variant-Somatic-Clinical-Trial
.... 20.293 variant-with-molec-consequences
.... 20.294 VariantExample
.... 20.295 VariantExample1
.... 20.296 VariantExample2
.... 20.297 WES-FullSequencedRegion-GRCh38
.... 20.298 WES-UncallableRegions-GRCh38
.... 20.299 ZFHX3-significance
.... 20.300 ZFHX3-uncertain-molc
.... 20.301 ZFHX3-uncertain-var