Genomics Reporting Implementation Guide (STU1)

Genomics Reporting Implementation Guide, published by HL7 International Clinical Genomics Work Group. This is not an authorized publication; it is the continuous build for version 1.0.0). 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

..0 Table of Contents
...1 IG Home Page
....1.1 Genomics Background
....1.2 General Genomic Reporting
....1.3 Variant Reporting
....1.4 Glossary
....1.5 Pharmacogenomic Reporting
....1.6 Somatic Reporting
....1.7 Histocompatibility and Immunogenetics Reporting
....1.8 Conversion from STU3
....1.9 Appendix A: Relation to v2 reporting
....1.10 Appendix B: Clinical Genomic Apps
....1.11 Appendix C: HL7 Domain Analysis Model
....1.12 Appendix D: External Coding Systems
...2 Artifact List
....2.1 Genomics Base
....2.2 Genomics Report
....2.3 Specimen
....2.4 Recommended Followup
....2.5 Request for Genomics Test
....2.6 Grouper
....2.7 Overall Interpretation
....2.8 Genomic Finding
....2.9 Haplotype
....2.10 Genotype
....2.11 Variant
....2.12 Sequence Phase Relationship
....2.13 Genomic Implication
....2.14 Inherited Disease Pathogenicity
....2.15 Region Studied
....2.16 Medication Implication
....2.17 Medication Metabolism Implication
....2.18 Medication Transporter Implication
....2.19 Medication Efficacy Implication
....2.20 High Risk Allele
....2.21 Medication Usage Implication
....2.22 Current Medication
....2.23 Somatic Implication
....2.24 Somatic Diagnostic Implication
....2.25 Somatic Prognostic Implication
....2.26 Somatic Predictive Implication
....2.27 Related Artifact
....2.28 Recommended Action
....2.29 Supporting Information
....2.30 Example - Genomics Reporting
....2.31 Example - Pharmacogenomics
....2.32 Example - Full Bundle HLA genotyping for HLA-A, HLA-B, and HLA-C, using GLStrings
....2.33 Example - CYP2C19 report from 1000 Genomes
....2.34 Example - subset of CYP2C19 report from 1000 Genomes showing phase
....2.35 Example - Multiple Oncology Variant Report Example
....2.36 Example - Melanoma implication
....2.37 Example - Full Bundle Oncology Example
....2.38 Example - Complex Variant (HGVS)
....2.39 Example - Complex Variant (unpacked)
....2.40 Example - NGS
....2.41 Example - Variant with ACMG Screening
....2.42 Example - High Risk Allele (HLA-B*15:02)
....2.43 Example - Inherited Disease Pathogenicity
....2.44 Example - HLA genotyping for HLA-A, HLA-B, and HLA-C, using GLStrings
....2.45 Example - HLA genotyping for HLA-A, using GLStrings
....2.46 Example - Observation for a single HLA-A allele
....2.47 Example - Buccal swab for HLA typing
....2.48 Example - Service request for high-resolution HLA-A genotyping
....2.49 TBD Code System
....2.50 Sequence Phase Relationship
....2.51 HGVS Value Set
....2.52 HGNC Value Set
....2.53 TBD Value Set
....2.54 DNA Change Type
....2.55 Functional Annotations
....2.56 Sequence Phase Relationship
....2.57 Variant Inheritance
....2.58 Concept mapping for DNA Change Type
....2.59 Operation: $find-subject-variants
...3 Operations
...4 Query Examples
...5 Useful Downloads