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 Metadata
.... 21.27 Genotype
.... 21.28 Haplotype
.... 21.29 Medication Recommendation
.... 21.30 Molecular Biomarker
.... 21.31 Molecular Consequence
.... 21.32 Sequence Phase Relationship
.... 21.33 Therapeutic Implication
.... 21.34 Variant
.... 21.35 Coded Annotation
.... 21.36 Annotation Code
.... 21.37 Genomic Report Note
.... 21.38 Genomic Risk Assessment
.... 21.39 Knowledgebase Ancestry Group
.... 21.40 Medication Assessed reference to a FHIR resource
.... 21.41 Recommended Action
.... 21.42 Repeat Motif Order
.... 21.43 Therapy Assessed reference to a FHIR resource
.... 21.44 Coded Annotation Types
.... 21.45 Condition Inheritance Patterns
.... 21.46 DNA Change Type
.... 21.47 Evidence Level Examples
.... 21.48 Functional Effect Value Set
.... 21.49 Genetic Therapeutic Implications
.... 21.50 HUGO Gene Nomenclature Committee Gene Names (HGNC)
.... 21.51 Human Genome Variation Society (HGVS) Nomenclature
.... 21.52 Knowledge Base Version Codes
.... 21.53 Molecular Biomarker Categories
.... 21.54 Molecular Biomarker Codes
.... 21.55 Molecular Consequence Value Set
.... 21.56 Sequence Phase Relationships
.... 21.57 To Be Determined Value Set
.... 21.58 Variant Confidence Status
.... 21.59 ClinVar Evidence Level Example Codes
.... 21.60 Coded Annotation Type Codes
.... 21.61 Knowledge Base Codes
.... 21.62 Molecular Biomarker Ontology Codes
.... 21.63 PharmGKB Evidence Level Example Codes
.... 21.64 Sequence Phase Relationship Codes
.... 21.65 To Be Determined Codes
.... 21.66 Variant Confidence Status Codes
.... 21.67 DNA Change Type Map
.... 21.68 AnnotationExample
.... 21.69 ATR-insertion-molc
.... 21.70 ATR-insertion-significance
.... 21.71 ATR-insertion-var
.... 21.72 bundle-CG-IG-HLA-FullBundle-01
.... 21.73 bundle-cgexample
.... 21.74 bundle-cgexample-withGrouping
.... 21.75 bundle-complexVariant-nonHGVS
.... 21.76 bundle-compound-heterozygote
.... 21.77 bundle-CYP2C19
.... 21.78 bundle-oncology-diagnostic
.... 21.79 bundle-oncology-report-example
.... 21.80 bundle-oncologyexamples-r4
.... 21.81 bundle-oncologyexamples-r4-withGrouping
.... 21.82 bundle-pgxexample
.... 21.83 bundle-sequence-phase-relation-CYP2C19
.... 21.84 CGPatientExample01
.... 21.85 CNVAnalysis-called
.... 21.86 denovoChild
.... 21.87 denovoFather
.... 21.88 denovoMother
.... 21.89 diagnosticImplication-interact-smn1-smn2
.... 21.90 diagnosticreport-hla-glstring-r4
.... 21.91 EGFR-L858R-molc
.... 21.92 EGFR-L858R-significance
.... 21.93 EGFR-L858R-therapuDrug1
.... 21.94 EGFR-L858R-therapuDrug2
.... 21.95 EGFR-L858R-var
.... 21.96 eMERGEServiceRequest
.... 21.97 ExampleGermlineCNV
.... 21.98 ExampleGermlineDEL
.... 21.99 ExampleGermlineINV
.... 21.100 ExampleLab
.... 21.101 ExampleOrg
.... 21.102 ExamplePatient
.... 21.103 ExampleServiceRequest
.... 21.104 ExampleSomaticCNV
.... 21.105 ExampleSomaticDEL
.... 21.106 ExampleSomaticINV
.... 21.107 ExampleSpecimen
.... 21.108 FindALLPopulationSpecificVariantsOutput
.... 21.109 FindANYPopulationSpecificVariantsOutput
.... 21.110 FindPopulationDxImplicationsOutput
.... 21.111 FindPopulationMolecConseqOutput
.... 21.112 FindPopulationSpecificHaplotypesOutput
.... 21.113 FindPopulationStructuralIntersectingVariantsOutput
.... 21.114 FindPopulationStructuralSubsumingVariantsOutput
.... 21.115 FindPopulationTxImplicationsOutput
.... 21.116 FindStudyMetadataOutput
.... 21.117 FindSubjectDxImplicationsOutput
.... 21.118 FindSubjectHaplotypesOutput
.... 21.119 FindSubjectMolecConseqOutput
.... 21.120 FindSubjectSpecificHaplotypesOutput
.... 21.121 FindSubjectSpecificVariantsOutput
.... 21.122 FindSubjectStructuralIntersectingVariantsOutput
.... 21.123 FindSubjectStructuralSubsumingVariantsOutput
.... 21.124 FindSubjectTxImplicationsOutput
.... 21.125 FindSubjectVariantsOutput
.... 21.126 FullGenome-GRCh38
.... 21.127 genomicFileFatherBAM
.... 21.128 genomicFileMotherBAM
.... 21.129 genomicFileProbandBAM
.... 21.130 genomicFileProbandVCF
.... 21.131 genomicPatient
.... 21.132 GenomicReportExample01
.... 21.133 genomicServiceRequest
.... 21.134 GenomicServiceRequestExample01
.... 21.135 genomicSpecimen
.... 21.136 GenomicSpecimenExample01
.... 21.137 GenomicSpecimenExample02
.... 21.138 genomicstudy-trio2
.... 21.139 genomicVCFfile-cnv
.... 21.140 genomicVCFfile-simple
.... 21.141 Genotype-Clinical-Trial-Example-using-haplotypes
.... 21.142 genotype-hla-a-glstring-r4
.... 21.143 GenotypeExample1
.... 21.144 GenotypeExamplePharmVar
.... 21.145 GenRiskDiabetesT2
.... 21.146 GrouperEx01
.... 21.147 GrouperEx02
.... 21.148 GrouperEx03
.... 21.149 haplotype-hla-a-1-r4
.... 21.150 HaplotypeExamplePharmVar01
.... 21.151 HaplotypeExamplePharmVar02
.... 21.152 HaplotypeSet-Clinical-Trial-Example-1of2
.... 21.153 HaplotypeSet-Clinical-Trial-Example-2of2
.... 21.154 HER2byImmuneStainExample
.... 21.155 HER2byImmunoassayExample
.... 21.156 HG00403
.... 21.157 HLA-A-haplotype1
.... 21.158 HLA-A-haplotype2
.... 21.159 HLA-B-haplotype1
.... 21.160 HLA-B-haplotype2
.... 21.161 HLA-C-haplotype1
.... 21.162 HLA-C-haplotype2
.... 21.163 ISCN-CMLExample
.... 21.164 ISCN-CMLImplication
.... 21.165 ISCN-NormalExample
.... 21.166 lungMass
.... 21.167 MedicationRecommendationExample1
.... 21.168 MedicationStatementWarfarin
.... 21.169 MicrosatelliteInstabilityExample01
.... 21.170 molec-conseq1
.... 21.171 molec-conseq2
.... 21.172 molec-conseq3
.... 21.173 molec-conseq4
.... 21.174 MSH2-del-disease
.... 21.175 MSH2-del-molc
.... 21.176 MSH2-del-var
.... 21.177 MSIExample
.... 21.178 MultipleRepeatExpansions
.... 21.179 normalSpecimen
.... 21.180 NOTCH1-significance
.... 21.181 NOTCH1-uncertain-molc
.... 21.182 NOTCH1-uncertain-var
.... 21.183 NTHL1-snv-disease
.... 21.184 NTHL1-snv-molc
.... 21.185 NTHL1-snv-var
.... 21.186 obs-idh-ex
.... 21.187 obs1-interact-smn1-smn2
.... 21.188 obs2-interact-smn1-smn2
.... 21.189 orderingPractitioner
.... 21.190 pathologistPractitioner
.... 21.191 PDL1Example
.... 21.192 performingOrganization
.... 21.193 Pgx-geno-1001
.... 21.194 Pgx-geno-1002
.... 21.195 Pgx-geno-1003
.... 21.196 Pgx-var-1011
.... 21.197 Pgx-var-1012
.... 21.198 Pgx-var-1013
.... 21.199 Pgx-var-1014
.... 21.200 Pgx-var-1015
.... 21.201 Pgx-var-1016
.... 21.202 Pgx-var-1017
.... 21.203 Pgx-var-1018
.... 21.204 Pgx-var-1019
.... 21.205 Pgx-var-1020
.... 21.206 Pgx-var-1021
.... 21.207 PGxGenomicReportEMERGE
.... 21.208 PGxGenomicReportEMERGE-withGrouping
.... 21.209 PGXGenomicStudy
.... 21.210 PGxRecEx01
.... 21.211 PGxRecEx02
.... 21.212 PGxRecEx03
.... 21.213 PGxRecEx04
.... 21.214 PGxRecEx05
.... 21.215 PolyGenicDiagnosticImpExample
.... 21.216 pop-allele-freq
.... 21.217 practitioner02
.... 21.218 RepeatExpansion
.... 21.219 ROS1-Fusion
.... 21.220 ROS1-Fusion-disease
.... 21.221 ROS1-Fusion-therapuDrug
.... 21.222 ROS1-Fusion-therapuTrial
.... 21.223 ROS1-Fusion-var
.... 21.224 SequencePhaseRelationExample1
.... 21.225 SequencingProcedure
.... 21.226 servicerequest-hla-a-r4
.... 21.227 SimpleVariantAnalysis-called
.... 21.228 SNVexample
.... 21.229 somaticPatient
.... 21.230 somaticReport
.... 21.231 somaticServiceRequest
.... 21.232 somaticStudy
.... 21.233 somaticVCFfile
.... 21.234 specimen-hla-r4
.... 21.235 STAG2-insertion-molc
.... 21.236 STAG2-insertion-significance
.... 21.237 STAG2-insertion-var
.... 21.238 supervisorPractitioner
.... 21.239 Therapeutic-Implication-Clinical-Trial-2
.... 21.240 Therapeutic-Implication-Clinical-Trial-Somatic
.... 21.241 TherapeuticImplicationExample1
.... 21.242 therapuDrug1-interact-smn1-smn2
.... 21.243 therapuDrug2-interact-smn1-smn2
.... 21.244 therapuDrug3-interact-smn1-smn2
.... 21.245 TMB-therapuDrug
.... 21.246 TMBExample
.... 21.247 triodenovo-software
.... 21.248 TumorMutationBurdenExample01
.... 21.249 tumorSpecimen
.... 21.250 TxImp01
.... 21.251 TxImp02
.... 21.252 TxImp03
.... 21.253 TxImp04
.... 21.254 TxImp05
.... 21.255 TxImp06
.... 21.256 UncallableRegions
.... 21.257 Variant-Somatic-Clinical-Trial
.... 21.258 variant-with-molec-consequences
.... 21.259 VariantExample
.... 21.260 VariantExample1
.... 21.261 VariantExample2
.... 21.262 WES-FullSequencedRegion-GRCh38
.... 21.263 WES-UncallableRegions-GRCh38
.... 21.264 ZFHX3-significance
.... 21.265 ZFHX3-uncertain-molc
.... 21.266 ZFHX3-uncertain-var