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 Artifact List
.... 4.1 Find Population Diagnostic Implications
.... 4.2 Find Population Molecular Consequences
.... 4.3 Find Population Specific Haplotypes
.... 4.4 Find Population Specific Variants
.... 4.5 Find Population Structural Intersecting Variants
.... 4.6 Find Population Structural Subsuming Variants
.... 4.7 Find Population Treatment Implications
.... 4.8 Find Study Metadata
.... 4.9 Find Subject Diagnostic Implications
.... 4.10 Find Subject Haplotypes
.... 4.11 Find Subject Molecular Consequences
.... 4.12 Find Subject Specific Haplotypes
.... 4.13 Find Subject Specific Variants
.... 4.14 Find Subject Structural Intersecting Variants
.... 4.15 Find Subject Structural Subsuming Variants
.... 4.16 Find Subject Treatment Implications
.... 4.17 Find Subject Variants
.... 4.18 Genomic Base
.... 4.19 Genomic Finding
.... 4.20 Genomic Implication
.... 4.21 Diagnostic Implication
.... 4.22 Followup Recommendation
.... 4.23 Genomic Annotation
.... 4.24 Genomic Data File
.... 4.25 Genomic Report
.... 4.26 Genotype
.... 4.27 Haplotype
.... 4.28 Medication Recommendation
.... 4.29 Molecular Biomarker
.... 4.30 Molecular Consequence
.... 4.31 Sequence Phase Relationship
.... 4.32 Therapeutic Implication
.... 4.33 Variant
.... 4.34 Coded Annotation
.... 4.35 Annotation Code
.... 4.36 Genomic Report Note
.... 4.37 Genomic Risk Assessment
.... 4.38 KnowledgebaseAncestryGroup
.... 4.39 Medication Assessed reference to a FHIR resource
.... 4.40 Recommended Action
.... 4.41 Repeat Motif Order
.... 4.42 Therapy Assessed reference to a FHIR resource
.... 4.43 Coded Annotation Types
.... 4.44 Condition Inheritance Patterns
.... 4.45 DNA Change Type
.... 4.46 Evidence Level Examples
.... 4.47 Functional Effect Value Set
.... 4.48 Genetic Therapeutic Implications
.... 4.49 HUGO Gene Nomenclature Committee Gene Names (HGNC)
.... 4.50 Human Genome Variation Society (HGVS) Nomenclature
.... 4.51 Knowledge Base Version Codes
.... 4.52 Molecular Biomarker Categories
.... 4.53 Molecular Biomarker Codes
.... 4.54 Molecular Consequence Value Set
.... 4.55 Sequence Phase Relationships
.... 4.56 To Be Determined Value Set
.... 4.57 Variant Confidence Status
.... 4.58 ClinVar Evidence Level Example Codes
.... 4.59 Coded Annotation Type Codes
.... 4.60 Knowledge Base Codes
.... 4.61 Molecular Biomarker Ontology Codes
.... 4.62 PharmGKB Evidence Level Example Codes
.... 4.63 Sequence Phase Relationship Codes
.... 4.64 To Be Determined Codes
.... 4.65 Variant Confidence Status Codes
.... 4.66 DNA Change Type Map
.... 4.67 AnnotationExample
.... 4.68 ATR-insertion-molc
.... 4.69 ATR-insertion-significance
.... 4.70 ATR-insertion-var
.... 4.71 bundle-CG-IG-HLA-FullBundle-01
.... 4.72 bundle-cgexample
.... 4.73 bundle-cgexample-withGrouping
.... 4.74 bundle-complexVariant-nonHGVS
.... 4.75 bundle-compound-heterozygote
.... 4.76 bundle-CYP2C19
.... 4.77 bundle-oncology-diagnostic
.... 4.78 bundle-oncology-report-example
.... 4.79 bundle-oncologyexamples-r4
.... 4.80 bundle-oncologyexamples-r4-withGrouping
.... 4.81 bundle-pgxexample
.... 4.82 bundle-sequence-phase-relation-CYP2C19
.... 4.83 CGPatientExample01
.... 4.84 CNVAnalysis-called
.... 4.85 denovoChild
.... 4.86 denovoFather
.... 4.87 denovoMother
.... 4.88 diagnosticImplication-interact-smn1-smn2
.... 4.89 diagnosticreport-hla-glstring-r4
.... 4.90 EGFR-L858R-molc
.... 4.91 EGFR-L858R-significance
.... 4.92 EGFR-L858R-therapuDrug1
.... 4.93 EGFR-L858R-therapuDrug2
.... 4.94 EGFR-L858R-var
.... 4.95 eMERGEServiceRequest
.... 4.96 ExampleGermlineCNV
.... 4.97 ExampleGermlineDEL
.... 4.98 ExampleGermlineINV
.... 4.99 ExampleLab
.... 4.100 ExampleOrg
.... 4.101 ExamplePatient
.... 4.102 ExampleServiceRequest
.... 4.103 ExampleSomaticCNV
.... 4.104 ExampleSomaticDEL
.... 4.105 ExampleSomaticINV
.... 4.106 ExampleSpecimen
.... 4.107 FindALLPopulationSpecificVariantsOutput
.... 4.108 FindANYPopulationSpecificVariantsOutput
.... 4.109 FindPopulationDxImplicationsOutput
.... 4.110 FindPopulationMolecConseqOutput
.... 4.111 FindPopulationSpecificHaplotypesOutput
.... 4.112 FindPopulationStructuralIntersectingVariantsOutput
.... 4.113 FindPopulationStructuralSubsumingVariantsOutput
.... 4.114 FindPopulationTxImplicationsOutput
.... 4.115 FindStudyMetadataOutput
.... 4.116 FindSubjectDxImplicationsOutput
.... 4.117 FindSubjectHaplotypesOutput
.... 4.118 FindSubjectMolecConseqOutput
.... 4.119 FindSubjectSpecificHaplotypesOutput
.... 4.120 FindSubjectSpecificVariantsOutput
.... 4.121 FindSubjectStructuralIntersectingVariantsOutput
.... 4.122 FindSubjectStructuralSubsumingVariantsOutput
.... 4.123 FindSubjectTxImplicationsOutput
.... 4.124 FindSubjectVariantsOutput
.... 4.125 FullGenome-GRCh38
.... 4.126 genomicFileFatherBAM
.... 4.127 genomicFileMotherBAM
.... 4.128 genomicFileProbandBAM
.... 4.129 genomicFileProbandVCF
.... 4.130 genomicPatient
.... 4.131 GenomicReportExample01
.... 4.132 genomicServiceRequest
.... 4.133 GenomicServiceRequestExample01
.... 4.134 genomicSpecimen
.... 4.135 GenomicSpecimenExample01
.... 4.136 GenomicSpecimenExample02
.... 4.137 genomicstudy-trio2
.... 4.138 genomicVCFfile-cnv
.... 4.139 genomicVCFfile-simple
.... 4.140 Genotype-Clinical-Trial-Example-using-haplotypes
.... 4.141 genotype-hla-a-glstring-r4
.... 4.142 GenotypeExample1
.... 4.143 GenotypeExamplePharmVar
.... 4.144 GenRiskDiabetesT2
.... 4.145 GrouperEx01
.... 4.146 GrouperEx02
.... 4.147 GrouperEx03
.... 4.148 haplotype-hla-a-1-r4
.... 4.149 HaplotypeExamplePharmVar01
.... 4.150 HaplotypeExamplePharmVar02
.... 4.151 HaplotypeSet-Clinical-Trial-Example-1of2
.... 4.152 HaplotypeSet-Clinical-Trial-Example-2of2
.... 4.153 HER2byImmuneStainExample
.... 4.154 HER2byImmunoassayExample
.... 4.155 HG00403
.... 4.156 HLA-A-haplotype1
.... 4.157 HLA-A-haplotype2
.... 4.158 HLA-B-haplotype1
.... 4.159 HLA-B-haplotype2
.... 4.160 HLA-C-haplotype1
.... 4.161 HLA-C-haplotype2
.... 4.162 ISCN-CMLExample
.... 4.163 ISCN-CMLImplication
.... 4.164 ISCN-NormalExample
.... 4.165 lungMass
.... 4.166 MedicationRecommendationExample1
.... 4.167 MedicationStatementWarfarin
.... 4.168 MicrosatelliteInstabilityExample01
.... 4.169 molec-conseq1
.... 4.170 molec-conseq2
.... 4.171 molec-conseq3
.... 4.172 molec-conseq4
.... 4.173 MSH2-del-disease
.... 4.174 MSH2-del-molc
.... 4.175 MSH2-del-var
.... 4.176 MSIExample
.... 4.177 MultipleRepeatExpansions
.... 4.178 normalSpecimen
.... 4.179 NOTCH1-significance
.... 4.180 NOTCH1-uncertain-molc
.... 4.181 NOTCH1-uncertain-var
.... 4.182 NTHL1-snv-disease
.... 4.183 NTHL1-snv-molc
.... 4.184 NTHL1-snv-var
.... 4.185 obs-idh-ex
.... 4.186 obs1-interact-smn1-smn2
.... 4.187 obs2-interact-smn1-smn2
.... 4.188 orderingPractitioner
.... 4.189 pathologistPractitioner
.... 4.190 PDL1Example
.... 4.191 performingOrganization
.... 4.192 Pgx-geno-1001
.... 4.193 Pgx-geno-1002
.... 4.194 Pgx-geno-1003
.... 4.195 Pgx-var-1011
.... 4.196 Pgx-var-1012
.... 4.197 Pgx-var-1013
.... 4.198 Pgx-var-1014
.... 4.199 Pgx-var-1015
.... 4.200 Pgx-var-1016
.... 4.201 Pgx-var-1017
.... 4.202 Pgx-var-1018
.... 4.203 Pgx-var-1019
.... 4.204 Pgx-var-1020
.... 4.205 Pgx-var-1021
.... 4.206 PGxGenomicReportEMERGE
.... 4.207 PGxGenomicReportEMERGE-withGrouping
.... 4.208 PGXGenomicStudy
.... 4.209 PGxRecEx01
.... 4.210 PGxRecEx02
.... 4.211 PGxRecEx03
.... 4.212 PGxRecEx04
.... 4.213 PGxRecEx05
.... 4.214 PolyGenicDiagnosticImpExample
.... 4.215 pop-allele-freq
.... 4.216 practitioner02
.... 4.217 RepeatExpansion
.... 4.218 ROS1-Fusion
.... 4.219 ROS1-Fusion-disease
.... 4.220 ROS1-Fusion-therapuDrug
.... 4.221 ROS1-Fusion-therapuTrial
.... 4.222 ROS1-Fusion-var
.... 4.223 SequencePhaseRelationExample1
.... 4.224 SequencingProcedure
.... 4.225 servicerequest-hla-a-r4
.... 4.226 SimpleVariantAnalysis-called
.... 4.227 SNVexample
.... 4.228 somaticPatient
.... 4.229 somaticReport
.... 4.230 somaticServiceRequest
.... 4.231 somaticStudy
.... 4.232 somaticVCFfile
.... 4.233 specimen-hla-r4
.... 4.234 STAG2-insertion-molc
.... 4.235 STAG2-insertion-significance
.... 4.236 STAG2-insertion-var
.... 4.237 supervisorPractitioner
.... 4.238 Therapeutic-Implication-Clinical-Trial-2
.... 4.239 Therapeutic-Implication-Clinical-Trial-Somatic
.... 4.240 TherapeuticImplicationExample1
.... 4.241 therapuDrug1-interact-smn1-smn2
.... 4.242 therapuDrug2-interact-smn1-smn2
.... 4.243 therapuDrug3-interact-smn1-smn2
.... 4.244 TMB-therapuDrug
.... 4.245 TMBExample
.... 4.246 triodenovo-software
.... 4.247 TumorMutationBurdenExample01
.... 4.248 tumorSpecimen
.... 4.249 TxImp01
.... 4.250 TxImp02
.... 4.251 TxImp03
.... 4.252 TxImp04
.... 4.253 TxImp05
.... 4.254 TxImp06
.... 4.255 UncallableRegions
.... 4.256 Variant-Somatic-Clinical-Trial
.... 4.257 variant-with-molec-consequences
.... 4.258 VariantExample
.... 4.259 VariantExample1
.... 4.260 VariantExample2
.... 4.261 WES-FullSequencedRegion-GRCh38
.... 4.262 WES-UncallableRegions-GRCh38
.... 4.263 ZFHX3-significance
.... 4.264 ZFHX3-uncertain-molc
.... 4.265 ZFHX3-uncertain-var
... 5 Variant 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