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-prequel-prenatal-trisomy13
.... 21.84 bundle-sequence-phase-relation-CYP2C19
.... 21.85 CGPatientExample01
.... 21.86 CNVAnalysis-called
.... 21.87 denovoChild
.... 21.88 denovoFather
.... 21.89 denovoMother
.... 21.90 diagnosticImplication-interact-smn1-smn2
.... 21.91 diagnosticreport-hla-glstring-r4
.... 21.92 EGFR-L858R-molc
.... 21.93 EGFR-L858R-significance
.... 21.94 EGFR-L858R-therapuDrug1
.... 21.95 EGFR-L858R-therapuDrug2
.... 21.96 EGFR-L858R-var
.... 21.97 eMERGEServiceRequest
.... 21.98 ExampleGermlineCNV
.... 21.99 ExampleGermlineDEL
.... 21.100 ExampleGermlineINV
.... 21.101 ExampleLab
.... 21.102 ExampleOrg
.... 21.103 ExamplePatient
.... 21.104 ExampleServiceRequest
.... 21.105 ExampleSomaticCNV
.... 21.106 ExampleSomaticDEL
.... 21.107 ExampleSomaticINV
.... 21.108 ExampleSpecimen
.... 21.109 FindALLPopulationSpecificVariantsOutput
.... 21.110 FindANYPopulationSpecificVariantsOutput
.... 21.111 FindPopulationDxImplicationsOutput
.... 21.112 FindPopulationMolecConseqOutput
.... 21.113 FindPopulationSpecificHaplotypesOutput
.... 21.114 FindPopulationStructuralIntersectingVariantsOutput
.... 21.115 FindPopulationStructuralSubsumingVariantsOutput
.... 21.116 FindPopulationTxImplicationsOutput
.... 21.117 FindStudyMetadataOutput
.... 21.118 FindSubjectDxImplicationsOutput
.... 21.119 FindSubjectHaplotypesOutput
.... 21.120 FindSubjectMolecConseqOutput
.... 21.121 FindSubjectSpecificHaplotypesOutput
.... 21.122 FindSubjectSpecificVariantsOutput
.... 21.123 FindSubjectStructuralIntersectingVariantsOutput
.... 21.124 FindSubjectStructuralSubsumingVariantsOutput
.... 21.125 FindSubjectTxImplicationsOutput
.... 21.126 FindSubjectVariantsOutput
.... 21.127 FullGenome-GRCh38
.... 21.128 genomicFileFatherBAM
.... 21.129 genomicFileMotherBAM
.... 21.130 genomicFileProbandBAM
.... 21.131 genomicFileProbandVCF
.... 21.132 genomicPatient
.... 21.133 GenomicReportExample01
.... 21.134 genomicServiceRequest
.... 21.135 GenomicServiceRequestExample01
.... 21.136 genomicSpecimen
.... 21.137 GenomicSpecimenExample01
.... 21.138 GenomicSpecimenExample02
.... 21.139 genomicstudy-trio2
.... 21.140 genomicVCFfile-cnv
.... 21.141 genomicVCFfile-simple
.... 21.142 Genotype-Clinical-Trial-Example-using-haplotypes
.... 21.143 genotype-hla-a-glstring-r4
.... 21.144 GenotypeExample1
.... 21.145 GenotypeExamplePharmVar
.... 21.146 GenRiskDiabetesT2
.... 21.147 GrouperEx01
.... 21.148 GrouperEx02
.... 21.149 GrouperEx03
.... 21.150 haplotype-hla-a-1-r4
.... 21.151 HaplotypeExamplePharmVar01
.... 21.152 HaplotypeExamplePharmVar02
.... 21.153 HaplotypeSet-Clinical-Trial-Example-1of2
.... 21.154 HaplotypeSet-Clinical-Trial-Example-2of2
.... 21.155 HER2byImmuneStainExample
.... 21.156 HER2byImmunoassayExample
.... 21.157 HG00403
.... 21.158 HLA-A-haplotype1
.... 21.159 HLA-A-haplotype2
.... 21.160 HLA-B-haplotype1
.... 21.161 HLA-B-haplotype2
.... 21.162 HLA-C-haplotype1
.... 21.163 HLA-C-haplotype2
.... 21.164 ISCN-CMLExample
.... 21.165 ISCN-CMLImplication
.... 21.166 ISCN-NormalExample
.... 21.167 lungMass
.... 21.168 MedicationRecommendationExample1
.... 21.169 MedicationStatementWarfarin
.... 21.170 MicrosatelliteInstabilityExample01
.... 21.171 molec-conseq1
.... 21.172 molec-conseq2
.... 21.173 molec-conseq3
.... 21.174 molec-conseq4
.... 21.175 MSH2-del-disease
.... 21.176 MSH2-del-molc
.... 21.177 MSH2-del-var
.... 21.178 MSIExample
.... 21.179 MultipleRepeatExpansions
.... 21.180 normalSpecimen
.... 21.181 NOTCH1-significance
.... 21.182 NOTCH1-uncertain-molc
.... 21.183 NOTCH1-uncertain-var
.... 21.184 NTHL1-snv-disease
.... 21.185 NTHL1-snv-molc
.... 21.186 NTHL1-snv-var
.... 21.187 obs-idh-ex
.... 21.188 obs1-interact-smn1-smn2
.... 21.189 obs2-interact-smn1-smn2
.... 21.190 orderingPractitioner
.... 21.191 pathologistPractitioner
.... 21.192 PDL1Example
.... 21.193 performingOrganization
.... 21.194 Pgx-geno-1001
.... 21.195 Pgx-geno-1002
.... 21.196 Pgx-geno-1003
.... 21.197 Pgx-var-1011
.... 21.198 Pgx-var-1012
.... 21.199 Pgx-var-1013
.... 21.200 Pgx-var-1014
.... 21.201 Pgx-var-1015
.... 21.202 Pgx-var-1016
.... 21.203 Pgx-var-1017
.... 21.204 Pgx-var-1018
.... 21.205 Pgx-var-1019
.... 21.206 Pgx-var-1020
.... 21.207 Pgx-var-1021
.... 21.208 PGxGenomicReportEMERGE
.... 21.209 PGxGenomicReportEMERGE-withGrouping
.... 21.210 PGXGenomicStudy
.... 21.211 PGxRecEx01
.... 21.212 PGxRecEx02
.... 21.213 PGxRecEx03
.... 21.214 PGxRecEx04
.... 21.215 PGxRecEx05
.... 21.216 PolyGenicDiagnosticImpExample
.... 21.217 pop-allele-freq
.... 21.218 practitioner02
.... 21.219 RepeatExpansion
.... 21.220 ROS1-Fusion
.... 21.221 ROS1-Fusion-disease
.... 21.222 ROS1-Fusion-therapuDrug
.... 21.223 ROS1-Fusion-therapuTrial
.... 21.224 ROS1-Fusion-var
.... 21.225 SequencePhaseRelationExample1
.... 21.226 SequencingProcedure
.... 21.227 servicerequest-hla-a-r4
.... 21.228 SimpleVariantAnalysis-called
.... 21.229 SNVexample
.... 21.230 somaticPatient
.... 21.231 somaticReport
.... 21.232 somaticServiceRequest
.... 21.233 somaticStudy
.... 21.234 somaticVCFfile
.... 21.235 specimen-hla-r4
.... 21.236 STAG2-insertion-molc
.... 21.237 STAG2-insertion-significance
.... 21.238 STAG2-insertion-var
.... 21.239 supervisorPractitioner
.... 21.240 Therapeutic-Implication-Clinical-Trial-2
.... 21.241 Therapeutic-Implication-Clinical-Trial-Somatic
.... 21.242 TherapeuticImplicationExample1
.... 21.243 therapuDrug1-interact-smn1-smn2
.... 21.244 therapuDrug2-interact-smn1-smn2
.... 21.245 therapuDrug3-interact-smn1-smn2
.... 21.246 TMB-therapuDrug
.... 21.247 TMBExample
.... 21.248 triodenovo-software
.... 21.249 TumorMutationBurdenExample01
.... 21.250 tumorSpecimen
.... 21.251 TxImp01
.... 21.252 TxImp02
.... 21.253 TxImp03
.... 21.254 TxImp04
.... 21.255 TxImp05
.... 21.256 TxImp06
.... 21.257 UncallableRegions
.... 21.258 Variant-Somatic-Clinical-Trial
.... 21.259 variant-with-molec-consequences
.... 21.260 VariantExample
.... 21.261 VariantExample1
.... 21.262 VariantExample2
.... 21.263 WES-FullSequencedRegion-GRCh38
.... 21.264 WES-UncallableRegions-GRCh38
.... 21.265 ZFHX3-significance
.... 21.266 ZFHX3-uncertain-molc
.... 21.267 ZFHX3-uncertain-var
... 22 Supporting Info Extension (Compatibility)