Genomics Reporting Implementation Guide
1.1.0 - Ballot

This page is part of the Genetic Reporting Implementation Guide (v1.1.0: STU 2 Ballot 1) based on FHIR R4. The current version which supercedes this version is 2.0.0. For a full list of available versions, see the Directory of published versions

Table of Contents

..0 Table of Contents
...1 IG Home Page
....1.1 Genomics Background
....1.2 General Genomic Reporting
....1.3 Variant Reporting
....1.4 Pharmacogenomic Reporting
....1.5 Somatic Reporting
....1.6 Histocompatibility and Immunogenetics Reporting
....1.7 Appendix A: Relation to v2 reporting
....1.8 Appendix B: Clinical Genomic Apps
....1.9 Appendix C: HL7 Domain Analysis Model
....1.10 Appendix D: External Coding Systems
....1.11 Appendix E: Conversion from STU3 Extensions
....1.12 Appendix F: Molecular Sequence
....1.13 Appendix G: Glossary
...2 Artifact List
....2.1 Request for Genomics Test
....2.2 Specimen
....2.3 Genomics Report
....2.4 Region Studied
....2.5 Grouper
....2.6 Overall Interpretation
....2.7 Haplotype
....2.8 Genotype
....2.9 Variant
....2.10 Sequence Phase Relationship
....2.11 Tumor mutation burden
....2.12 Microsatellite instability
....2.13 Diagnostic Implication
....2.14 Therapeutic Implication
....2.15 Medication Usage Task
....2.16 Recommended Followup
....2.17 Genomics Base
....2.18 Genomic Finding
....2.19 Genomic Implication
....2.20 Related Artifact
....2.21 Recommended Action
....2.22 Supporting Information
....2.23 TBD Code System
....2.24 Sequence Phase Relationship
....2.25 High/Low codes
....2.26 HGVS Value Set
....2.27 HGNC Value Set
....2.28 TBD Value Set
....2.29 DNA Change Type
....2.30 Molecular Consequence
....2.31 Sequence Phase Relationship
....2.32 Variant Inheritance
....2.33 Concept mapping for DNA Change Type
....2.34 Operation: $find-subject-variants
....2.35 Example Org
....2.36 Example - TherapeuticImplication
....2.37 Example - Genotype
....2.38 Example - TaskMedChg
....2.39 Example - GenomicsReport
....2.40 Example - Sequence Phase Relation
....2.41 Example - Overall Interpretation
....2.42 Example - TMB
....2.43 Example - MSI
....2.44 Example - Service Request
....2.45 Example - Variant1
....2.46 Example - Variant2
....2.47 Example - Patient
....2.48 Example - Specimen
....2.49 Example - Observation PGx Genotype 1
....2.50 Example - Observation PGx Genotype 2
....2.51 Example - Observation PGx Genotype 3
....2.52 Example - Observation PGx interpretation
....2.53 Example - Observation-GrouperEx01
....2.54 Example - Observation-GrouperEx02
....2.55 Example - Observation-GrouperEx03
....2.56 Example - DiagnosticReport-PGxGenomicsReportEMERGE
....2.57 Example - Observation-Pgx-var-1011
....2.58 Example - Observation-Pgx-var-1012
....2.59 Example - Observation-Pgx-var-1013
....2.60 Example - Observation-Pgx-var-1014
....2.61 Example - Observation-Pgx-var-1015
....2.62 Example - Observation-Pgx-var-1016
....2.63 Example - Observation-Pgx-var-1017
....2.64 Example - Observation-Pgx-var-1018
....2.65 Example - Observation-Pgx-var-1019
....2.66 Example - Observation-Pgx-var-1020
....2.67 Example - Observation-Pgx-var-1021
....2.68 Example - Observation-RegionStudiedPGx1
....2.69 Example - Observation-RegionStudiedPGx2
....2.70 Example - Observation-RegionStudiedPGx3
....2.71 Example - Observation-TxImp01
....2.72 Example - Observation-TxImp02
....2.73 Example - Observation-TxImp03
....2.74 Example - Observation-TxImp04
....2.75 Example - Observation-TxImp05
....2.76 Example - Observation-TxImp06
....2.77 Example - ServiceRequest-eMERGEServiceRequest
....2.78 Example - Genomics Reporting
....2.79 Example - Complex Variant (HGVS)
....2.80 Example - Complex Variant (unpacked)
....2.81 Example - NGS
....2.82 Example - ACMG Screening result
....2.83 Example - Inherited Disease Pathogenicity
....2.84 Example - Pharmacogenomics
....2.85 Example - CYP2C19 report from 1000 Genomes
....2.86 Example - subset of CYP2C19 report from 1000 Genomes showing phase
....2.87 Example - Full Bundle HLA genotyping for HLA-A, HLA-B, and HLA-C, using GLStrings
....2.88 Example - HLA genotyping for HLA-A, HLA-B, and HLA-C, using GLStrings
....2.89 Example - HLA genotyping for HLA-A, using GLStrings
....2.90 Example - Observation for a single HLA-A allele
....2.91 Example - Buccal swab for HLA typing
....2.92 Example - Service request for high-resolution HLA-A genotyping
....2.93 Example - Multiple Oncology Variant Report Example
....2.94 Example - Melanoma implication
....2.95 Example - Full Bundle Oncology Example
....2.96 Risk Assessment Reference
....2.97 Condition Inheritance Pattern
....2.98 Functional Effect
....2.99 Condition Inheritance Pattern
....2.100 Example Task - PGxRecEx01
....2.101 Example Task - PGxRecEx02
....2.102 Example Task - PGxRecEx03
....2.103 Example Task - PGxRecEx04
....2.104 Example Task - PGxRecEx05
...3 Operations
...4 Query Examples
...5 Useful Downloads