  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 FindPopulationSpecificVariantsGroupOutput |
| 21.144 FindPopulationStructuralIntersectingVariantsOutput |
| 21.145 FindPopulationStructuralSubsumingVariantsOutput |
| 21.146 FindPopulationTxImplicationsOutput |
| 21.147 FindStudyMetadataOutput |
| 21.148 FindSubjectDxImplicationsOutput |
| 21.149 FindSubjectHaplotypesOutput |
| 21.150 FindSubjectMolecConseqOutput |
| 21.151 FindSubjectSpecificHaplotypesOutput |
| 21.152 FindSubjectSpecificVariantsOutput |
| 21.153 FindSubjectStructuralIntersectingVariantsOutput |
| 21.154 FindSubjectStructuralSubsumingVariantsOutput |
| 21.155 FindSubjectTxImplicationsOutput |
| 21.156 FindSubjectVariantsOutput |
| 21.157 FullGenome-GRCh38 |
| 21.158 genomicFileFatherBAM |
| 21.159 genomicFileMotherBAM |
| 21.160 genomicFileProbandBAM |
| 21.161 genomicFileProbandVCF |
| 21.162 genomicPatient |
| 21.163 GenomicReportExample01 |
| 21.164 genomicServiceRequest |
| 21.165 GenomicServiceRequestExample01 |
| 21.166 genomicSpecimen |
| 21.167 GenomicSpecimenExample01 |
| 21.168 GenomicSpecimenExample02 |
| 21.169 genomicstudy-trio2 |
| 21.170 genomicstudyanalysis-trio2 |
| 21.171 genomicVCFfile-cnv |
| 21.172 genomicVCFfile-simple |
| 21.173 Genotype-Clinical-Trial-Example-using-haplotypes |
| 21.174 genotype-hla-a-glstring-r4 |
| 21.175 GenotypeExample1 |
| 21.176 GenotypeExamplePharmVar |
| 21.177 GenRiskDiabetesT2 |
| 21.178 GrouperEx01 |
| 21.179 GrouperEx02 |
| 21.180 GrouperEx03 |
| 21.181 haplotype-hla-a-1-r4 |
| 21.182 HaplotypeExamplePharmVar01 |
| 21.183 HaplotypeExamplePharmVar02 |
| 21.184 HaplotypeSet-Clinical-Trial-Example-1of2 |
| 21.185 HaplotypeSet-Clinical-Trial-Example-2of2 |
| 21.186 HER2byImmuneStainExample |
| 21.187 HER2byImmunoassayExample |
| 21.188 HG00403 |
| 21.189 HLA-A-haplotype1 |
| 21.190 HLA-A-haplotype2 |
| 21.191 HLA-B-haplotype1 |
| 21.192 HLA-B-haplotype2 |
| 21.193 HLA-C-haplotype1 |
| 21.194 HLA-C-haplotype2 |
| 21.195 ISCN-CMLExample |
| 21.196 ISCN-CMLImplication |
| 21.197 ISCN-NormalExample |
| 21.198 lungMass |
| 21.199 lungMass-analysis1 |
| 21.200 lungMass-analysis2 |
| 21.201 MedicationRecommendationExample1 |
| 21.202 MedicationStatementWarfarin |
| 21.203 MicrosatelliteInstabilityExample01 |
| 21.204 molec-conseq1 |
| 21.205 molec-conseq2 |
| 21.206 molec-conseq3 |
| 21.207 molec-conseq4 |
| 21.208 MSH2-del-disease |
| 21.209 MSH2-del-molc |
| 21.210 MSH2-del-var |
| 21.211 MSIExample |
| 21.212 MultipleRepeatExpansions |
| 21.213 normalSpecimen |
| 21.214 NOTCH1-significance |
| 21.215 NOTCH1-uncertain-molc |
| 21.216 NOTCH1-uncertain-var |
| 21.217 NTHL1-snv-disease |
| 21.218 NTHL1-snv-molc |
| 21.219 NTHL1-snv-var |
| 21.220 obs-idh-ex |
| 21.221 obs1-interact-smn1-smn2 |
| 21.222 obs2-interact-smn1-smn2 |
| 21.223 orderingPractitioner |
| 21.224 pathologistPractitioner |
| 21.225 PDL1Example |
| 21.226 performingOrganization |
| 21.227 Pgx-geno-1001 |
| 21.228 Pgx-geno-1002 |
| 21.229 Pgx-geno-1003 |
| 21.230 Pgx-var-1011 |
| 21.231 Pgx-var-1012 |
| 21.232 Pgx-var-1013 |
| 21.233 Pgx-var-1014 |
| 21.234 Pgx-var-1015 |
| 21.235 Pgx-var-1016 |
| 21.236 Pgx-var-1017 |
| 21.237 Pgx-var-1018 |
| 21.238 Pgx-var-1019 |
| 21.239 Pgx-var-1020 |
| 21.240 Pgx-var-1021 |
| 21.241 PGxGenomicReportEMERGE |
| 21.242 PGxGenomicReportEMERGE-withGrouping |
| 21.243 PGXGenomicStudy |
| 21.244 PGXGenomicStudyAnalysis |
| 21.245 PGxRecEx01 |
| 21.246 PGxRecEx02 |
| 21.247 PGxRecEx03 |
| 21.248 PGxRecEx04 |
| 21.249 PGxRecEx05 |
| 21.250 PolyGenicDiagnosticImpExample |
| 21.251 pop-allele-freq |
| 21.252 practitioner02 |
| 21.253 RepeatExpansion |
| 21.254 ROS1-Fusion |
| 21.255 ROS1-Fusion-disease |
| 21.256 ROS1-Fusion-therapuDrug |
| 21.257 ROS1-Fusion-therapuTrial |
| 21.258 ROS1-Fusion-var |
| 21.259 SequencePhaseRelationExample1 |
| 21.260 SequencingProcedure |
| 21.261 servicerequest-hla-a-r4 |
| 21.262 SimpleVariantAnalysis-called |
| 21.263 SNVexample |
| 21.264 somaticPatient |
| 21.265 somaticReport |
| 21.266 somaticServiceRequest |
| 21.267 somaticStudy |
| 21.268 somaticVCFfile |
| 21.269 specimen-hla-r4 |
| 21.270 STAG2-insertion-molc |
| 21.271 STAG2-insertion-significance |
| 21.272 STAG2-insertion-var |
| 21.273 supervisorPractitioner |
| 21.274 Therapeutic-Implication-Clinical-Trial-2 |
| 21.275 Therapeutic-Implication-Clinical-Trial-Somatic |
| 21.276 TherapeuticImplicationExample1 |
| 21.277 therapuDrug1-interact-smn1-smn2 |
| 21.278 therapuDrug2-interact-smn1-smn2 |
| 21.279 therapuDrug3-interact-smn1-smn2 |
| 21.280 TMB-therapuDrug |
| 21.281 TMBExample |
| 21.282 triodenovo-software |
| 21.283 TumorMutationBurdenExample01 |
| 21.284 tumorSpecimen |
| 21.285 TxImp01 |
| 21.286 TxImp02 |
| 21.287 TxImp03 |
| 21.288 TxImp04 |
| 21.289 TxImp05 |
| 21.290 TxImp06 |
| 21.291 UncallableRegions |
| 21.292 Variant-Somatic-Clinical-Trial |
| 21.293 variant-with-molec-consequences |
| 21.294 VariantExample |
| 21.295 VariantExample1 |
| 21.296 VariantExample2 |
| 21.297 WES-FullSequencedRegion-GRCh38 |
| 21.298 WES-UncallableRegions-GRCh38 |
| 21.299 ZFHX3-significance |
| 21.300 ZFHX3-uncertain-molc |
 21.301 ZFHX3-uncertain-var |
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