Genomics Reporting Implementation Guide
4.0.0-cibuild - CI Build 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-cibuild 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 Cytogenomic Reporting
... 6 Pharmacogenomic Reporting
... 7 Somatic Reporting
... 8 Histocompatibility and Immunogenetic Reporting
... 9 Genomic Operations
... 10 Useful Downloads
... 11 Appendix A: Relation to v2 reporting
... 12 Appendix B: Clinical Genomic Apps
... 13 Appendix C: HL7 Domain Analysis Model
... 14 Appendix D: Query Guidance
... 15 Appendix E: External Coding Systems
... 16 Appendix F: Conversion from FHIR Core STU3
... 17 Appendix G: Molecular Sequence
... 18 Appendix H: Grouping Guidance
... 19 Appendix I: Glossary
... 20 Change Log
... 21 Artifact List
.... 21.1 Find Population Diagnostic Implications
.... 21.2 Find Population Molecular Consequences
.... 21.3 Find Population Specific Haplotypes
.... 21.4 Find Population Specific Variants
.... 21.5 Find Population Structural Intersecting Variants
.... 21.6 Find Population Structural Subsuming Variants
.... 21.7 Find Population Treatment Implications
.... 21.8 Find Study Metadata
.... 21.9 Find Subject Diagnostic Implications
.... 21.10 Find Subject Haplotypes
.... 21.11 Find Subject Molecular Consequences
.... 21.12 Find Subject Specific Haplotypes
.... 21.13 Find Subject Specific Variants
.... 21.14 Find Subject Structural Intersecting Variants
.... 21.15 Find Subject Structural Subsuming Variants
.... 21.16 Find Subject Treatment Implications
.... 21.17 Find Subject Variants
.... 21.18 Genomic Base
.... 21.19 Genomic Finding
.... 21.20 Genomic Implication
.... 21.21 Diagnostic Implication
.... 21.22 Followup Recommendation
.... 21.23 Genomic Annotation
.... 21.24 Genomic Data File
.... 21.25 Genomic Report
.... 21.26 Genomic Study
.... 21.27 Genomic Study Analysis
.... 21.28 Genotype
.... 21.29 Haplotype
.... 21.30 Medication Recommendation
.... 21.31 Molecular Biomarker
.... 21.32 Molecular Consequence
.... 21.33 Sequence Phase Relationship
.... 21.34 Therapeutic Implication
.... 21.35 Variant
.... 21.36 Coded Annotation
.... 21.37 Annotation Code
.... 21.38 Genomic Report Note
.... 21.39 Genomic Risk Assessment
.... 21.40 Genomic Study Analysis Change Type
.... 21.41 Genomic Study Analysis Device
.... 21.42 Genomic Study Analysis Extension
.... 21.43 Genomic Study Analysis Focus
.... 21.44 Genomic Study Analysis Genome Build
.... 21.45 Genomic Study Analysis Input
.... 21.46 Genomic Study Analysis Method Type
.... 21.47 Genomic Study Analysis Metrics
.... 21.48 Genomic Study Analysis Output
.... 21.49 Genomic Study Analysis Protocol Performed
.... 21.50 Genomic Study Analysis Regions
.... 21.51 Genomic Study Analysis Source Class
.... 21.52 Genomic Study Analysis Specimen
.... 21.53 Genomic Study Analysis Title
.... 21.54 Genomic Study Reference
.... 21.55 Genomic Study Referrer Extension
.... 21.56 Knowledgebase Ancestry Group
.... 21.57 Medication Assessed reference to a FHIR resource
.... 21.58 Recommended Action
.... 21.59 Repeat Motif Order
.... 21.60 Therapy Assessed reference to a FHIR resource
.... 21.61 Coded Annotation Types
.... 21.62 Condition Inheritance Patterns
.... 21.63 DNA Change Type
.... 21.64 Evidence Level Examples
.... 21.65 Functional Effect Value Set
.... 21.66 Genetic Therapeutic Implications
.... 21.67 Genomic Study Change Type ValueSet
.... 21.68 Genomic Study Data Format ValueSet
.... 21.69 Genomic Study Method Type ValueSet
.... 21.70 Genomic Study Status ValueSet
.... 21.71 Genomic Study Type ValueSet
.... 21.72 HUGO Gene Nomenclature Committee Gene Names (HGNC)
.... 21.73 Human Genome Variation Society (HGVS) Nomenclature
.... 21.74 Knowledge Base Version Codes
.... 21.75 Molecular Biomarker Categories
.... 21.76 Molecular Biomarker Codes
.... 21.77 Molecular Consequence Value Set
.... 21.78 Sequence Phase Relationships
.... 21.79 To Be Determined Value Set
.... 21.80 Variant Confidence Status
.... 21.81 ClinVar Evidence Level Example Codes
.... 21.82 Coded Annotation Type Codes
.... 21.83 Genomic Study Change Type CodeSystem
.... 21.84 Genomic Study Data Format CodeSystem
.... 21.85 Genomic Study Method Type CodeSystem
.... 21.86 Genomic Study Status CodeSystem
.... 21.87 Genomic Study Type CodeSystem
.... 21.88 Knowledge Base Codes
.... 21.89 Molecular Biomarker Ontology Codes
.... 21.90 PharmGKB Evidence Level Example Codes
.... 21.91 Sequence Phase Relationship Codes
.... 21.92 To Be Determined Codes
.... 21.93 Variant Confidence Status Codes
.... 21.94 DNA Change Type Map
.... 21.95 Genomic Study Status Map
.... 21.96 analysisTumorNormalDNA
.... 21.97 analysisTumorRNA
.... 21.98 AnnotationExample
.... 21.99 ATR-insertion-molc
.... 21.100 ATR-insertion-significance
.... 21.101 ATR-insertion-var
.... 21.102 bundle-CG-IG-HLA-FullBundle-01
.... 21.103 bundle-cgexample
.... 21.104 bundle-cgexample-withGrouping
.... 21.105 bundle-complexVariant-nonHGVS
.... 21.106 bundle-compound-heterozygote
.... 21.107 bundle-CYP2C19
.... 21.108 bundle-oncology-diagnostic
.... 21.109 bundle-oncology-report-example
.... 21.110 bundle-oncologyexamples-r4
.... 21.111 bundle-oncologyexamples-r4-withGrouping
.... 21.112 bundle-pgxexample
.... 21.113 bundle-sequence-phase-relation-CYP2C19
.... 21.114 CGPatientExample01
.... 21.115 CNVAnalysis-called
.... 21.116 denovoChild
.... 21.117 denovoFather
.... 21.118 denovoMother
.... 21.119 diagnosticImplication-interact-smn1-smn2
.... 21.120 diagnosticreport-hla-glstring-r4
.... 21.121 EGFR-L858R-molc
.... 21.122 EGFR-L858R-significance
.... 21.123 EGFR-L858R-therapuDrug1
.... 21.124 EGFR-L858R-therapuDrug2
.... 21.125 EGFR-L858R-var
.... 21.126 eMERGEServiceRequest
.... 21.127 ExampleGermlineCNV
.... 21.128 ExampleGermlineDEL
.... 21.129 ExampleGermlineINV
.... 21.130 ExampleLab
.... 21.131 ExampleOrg
.... 21.132 ExamplePatient
.... 21.133 ExampleServiceRequest
.... 21.134 ExampleSomaticCNV
.... 21.135 ExampleSomaticDEL
.... 21.136 ExampleSomaticINV
.... 21.137 ExampleSpecimen
.... 21.138 FindALLPopulationSpecificVariantsOutput
.... 21.139 FindANYPopulationSpecificVariantsOutput
.... 21.140 FindPopulationDxImplicationsOutput
.... 21.141 FindPopulationMolecConseqOutput
.... 21.142 FindPopulationSpecificHaplotypesOutput
.... 21.143 FindPopulationStructuralIntersectingVariantsOutput
.... 21.144 FindPopulationStructuralSubsumingVariantsOutput
.... 21.145 FindPopulationTxImplicationsOutput
.... 21.146 FindStudyMetadataOutput
.... 21.147 FindSubjectDxImplicationsOutput
.... 21.148 FindSubjectHaplotypesOutput
.... 21.149 FindSubjectMolecConseqOutput
.... 21.150 FindSubjectSpecificHaplotypesOutput
.... 21.151 FindSubjectSpecificVariantsOutput
.... 21.152 FindSubjectStructuralIntersectingVariantsOutput
.... 21.153 FindSubjectStructuralSubsumingVariantsOutput
.... 21.154 FindSubjectTxImplicationsOutput
.... 21.155 FindSubjectVariantsOutput
.... 21.156 FullGenome-GRCh38
.... 21.157 genomicFileFatherBAM
.... 21.158 genomicFileMotherBAM
.... 21.159 genomicFileProbandBAM
.... 21.160 genomicFileProbandVCF
.... 21.161 genomicPatient
.... 21.162 GenomicReportExample01
.... 21.163 genomicServiceRequest
.... 21.164 GenomicServiceRequestExample01
.... 21.165 genomicSpecimen
.... 21.166 GenomicSpecimenExample01
.... 21.167 GenomicSpecimenExample02
.... 21.168 genomicstudy-trio2
.... 21.169 genomicstudyanalysis-trio2
.... 21.170 genomicVCFfile-cnv
.... 21.171 genomicVCFfile-simple
.... 21.172 Genotype-Clinical-Trial-Example-using-haplotypes
.... 21.173 genotype-hla-a-glstring-r4
.... 21.174 GenotypeExample1
.... 21.175 GenotypeExamplePharmVar
.... 21.176 GenRiskDiabetesT2
.... 21.177 GrouperEx01
.... 21.178 GrouperEx02
.... 21.179 GrouperEx03
.... 21.180 haplotype-hla-a-1-r4
.... 21.181 HaplotypeExamplePharmVar01
.... 21.182 HaplotypeExamplePharmVar02
.... 21.183 HaplotypeSet-Clinical-Trial-Example-1of2
.... 21.184 HaplotypeSet-Clinical-Trial-Example-2of2
.... 21.185 HER2byImmuneStainExample
.... 21.186 HER2byImmunoassayExample
.... 21.187 HG00403
.... 21.188 HLA-A-haplotype1
.... 21.189 HLA-A-haplotype2
.... 21.190 HLA-B-haplotype1
.... 21.191 HLA-B-haplotype2
.... 21.192 HLA-C-haplotype1
.... 21.193 HLA-C-haplotype2
.... 21.194 ISCN-CMLExample
.... 21.195 ISCN-CMLImplication
.... 21.196 ISCN-NormalExample
.... 21.197 lungMass
.... 21.198 lungMass-analysis1
.... 21.199 lungMass-analysis2
.... 21.200 MedicationRecommendationExample1
.... 21.201 MedicationStatementWarfarin
.... 21.202 MicrosatelliteInstabilityExample01
.... 21.203 molec-conseq1
.... 21.204 molec-conseq2
.... 21.205 molec-conseq3
.... 21.206 molec-conseq4
.... 21.207 MSH2-del-disease
.... 21.208 MSH2-del-molc
.... 21.209 MSH2-del-var
.... 21.210 MSIExample
.... 21.211 MultipleRepeatExpansions
.... 21.212 normalSpecimen
.... 21.213 NOTCH1-significance
.... 21.214 NOTCH1-uncertain-molc
.... 21.215 NOTCH1-uncertain-var
.... 21.216 NTHL1-snv-disease
.... 21.217 NTHL1-snv-molc
.... 21.218 NTHL1-snv-var
.... 21.219 obs-idh-ex
.... 21.220 obs1-interact-smn1-smn2
.... 21.221 obs2-interact-smn1-smn2
.... 21.222 orderingPractitioner
.... 21.223 pathologistPractitioner
.... 21.224 PDL1Example
.... 21.225 performingOrganization
.... 21.226 Pgx-geno-1001
.... 21.227 Pgx-geno-1002
.... 21.228 Pgx-geno-1003
.... 21.229 Pgx-var-1011
.... 21.230 Pgx-var-1012
.... 21.231 Pgx-var-1013
.... 21.232 Pgx-var-1014
.... 21.233 Pgx-var-1015
.... 21.234 Pgx-var-1016
.... 21.235 Pgx-var-1017
.... 21.236 Pgx-var-1018
.... 21.237 Pgx-var-1019
.... 21.238 Pgx-var-1020
.... 21.239 Pgx-var-1021
.... 21.240 PGxGenomicReportEMERGE
.... 21.241 PGxGenomicReportEMERGE-withGrouping
.... 21.242 PGXGenomicStudy
.... 21.243 PGXGenomicStudyAnalysis
.... 21.244 PGxRecEx01
.... 21.245 PGxRecEx02
.... 21.246 PGxRecEx03
.... 21.247 PGxRecEx04
.... 21.248 PGxRecEx05
.... 21.249 PolyGenicDiagnosticImpExample
.... 21.250 pop-allele-freq
.... 21.251 practitioner02
.... 21.252 RepeatExpansion
.... 21.253 ROS1-Fusion
.... 21.254 ROS1-Fusion-disease
.... 21.255 ROS1-Fusion-therapuDrug
.... 21.256 ROS1-Fusion-therapuTrial
.... 21.257 ROS1-Fusion-var
.... 21.258 SequencePhaseRelationExample1
.... 21.259 SequencingProcedure
.... 21.260 servicerequest-hla-a-r4
.... 21.261 SimpleVariantAnalysis-called
.... 21.262 SNVexample
.... 21.263 somaticPatient
.... 21.264 somaticReport
.... 21.265 somaticServiceRequest
.... 21.266 somaticStudy
.... 21.267 somaticVCFfile
.... 21.268 specimen-hla-r4
.... 21.269 STAG2-insertion-molc
.... 21.270 STAG2-insertion-significance
.... 21.271 STAG2-insertion-var
.... 21.272 supervisorPractitioner
.... 21.273 Therapeutic-Implication-Clinical-Trial-2
.... 21.274 Therapeutic-Implication-Clinical-Trial-Somatic
.... 21.275 TherapeuticImplicationExample1
.... 21.276 therapuDrug1-interact-smn1-smn2
.... 21.277 therapuDrug2-interact-smn1-smn2
.... 21.278 therapuDrug3-interact-smn1-smn2
.... 21.279 TMB-therapuDrug
.... 21.280 TMBExample
.... 21.281 triodenovo-software
.... 21.282 TumorMutationBurdenExample01
.... 21.283 tumorSpecimen
.... 21.284 TxImp01
.... 21.285 TxImp02
.... 21.286 TxImp03
.... 21.287 TxImp04
.... 21.288 TxImp05
.... 21.289 TxImp06
.... 21.290 UncallableRegions
.... 21.291 Variant-Somatic-Clinical-Trial
.... 21.292 variant-with-molec-consequences
.... 21.293 VariantExample
.... 21.294 VariantExample1
.... 21.295 VariantExample2
.... 21.296 WES-FullSequencedRegion-GRCh38
.... 21.297 WES-UncallableRegions-GRCh38
.... 21.298 ZFHX3-significance
.... 21.299 ZFHX3-uncertain-molc
.... 21.300 ZFHX3-uncertain-var