Genomics Reporting Implementation Guide
3.0.1-SNAPSHOT - 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 3.0.1-SNAPSHOT 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

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