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

Artifact List

Artifact Packages

This page provides a list of the FHIR artifacts defined as part of this implementation guide.

General Profiles

General constraints on FHIR resources to be adhered to as part of the CG implementation guide that apply regardless of what area(s) of genomics are of interest

  •  Genomics Report Defines the overall genomic report
  •  Specimen Constraints on Specimen for use with clinical genomics reporting
  •  Recommended Followup Task describing the followup that is recommended
  •  Request for Genomics Test The lab order or request that triggered the execution of the genomics test
  •  Grouper Organizes information within a genomic report
  •  Overall Interpretation Provides a coarse overall interpretation of the genomic results reported.
  •  Haplotype Assertion of a particular haplotype on the basis of one or more variants
  •  Genotype Assertion of a particular genotype on the basis of one or more variants or haplotypes
  •  Variant Details about a set of changes in the tested sample compared to a reference sequence.
  •  Sequence Phase Relationship Indicates whether two entities are in Cis (same strand) or Trans (opposite strand) relationship to each other
  •  Inherited Disease Pathogenicity Provides an indication of whether there's a pathologic risk associated with a particular genotype, haplotype, variant or combination there-of, and if so, what the associated pathology is.
  •  Region Studied Provides a description of the region studied.

Somatics

Profiles related to the reporting of somatic genomic issues

  •  Somatic Diagnostic Implication Finding of whether a particular somatic genotype/haplotype/variation or combination-thereof supports or opposes the diagnosis of a particular cancer
  •  Somatic Prognostic Implication Finding of whether a particular somatic genotype/haplotype/variation or combination-thereof predicts a particular outcome for the specified cancer - either on its own or in conjunction with one or more interventions
  •  Somatic Predictive Implication Finding of whether a particular somatic genotype/haplotype/variation or combination-thereof predicts the implication of a specified medication or combination of medications

Pharmacogenomics

Profiles for reports relating to genomic implication on medication use and effectiveness

  •  Medication Metabolism Implication Assertion of the expected implication of a particular genotype on the ability of the subject to metabolize medications
  •  Medication Transporter Implication Assertion of the expected implication of a particular genotype on the ability of the subject to actively transport medications
  •  Medication Efficacy Implication Assertion of the expected implication of a particular genotype on the efficacy of medications for the subject
  •  High Risk Allele Assertion of whether the patient has a high-risk allele
  •  Medication Usage Implication Task describing what sort of change (if any) should be made in a patient's medication based on an identified genotype
  •  Current Medication MedicationStatement describing a med potentially being taken by the patient that may require adjustment

Abstract

Abstract profiles holding common properties, outlining similarities in implementable profiles

  •  Genomics Base Base profile that defines characteristics shared by all genomic observations
  •  Genomic Finding Properties common to genomic findings whose results are expressed as computable discrete elements (e.g. genotypes, haplotypes, variants, etc.)
  •  Genomic Implication Abstract profile for observations describing the implication of one or more genomic observations.
  •  Medication Implication Abstract profile with common properties for observations that convey the potential implication of a genomic characteristics on a medication
  •  Somatic Implication Finding of whether a particular somatic genotype/haplotype/variation or combination-thereof provides evidence for or against a particular type of cancer or the effectiveness of different interventions

Extensions

Extensions defined as part of the CG implementation guide

  •  Related Artifact Captures citations, evidence and other supporting documentation for the observation or report
  •  Recommended Action References a proposed action that is recommended based on the results of the report or observations
  •  Supporting Information Additional information relevant to interpreting/understanding the report

Examples

Examples showing the use of the CG profiles

  •  Example - Genomics Reporting Test instance showing data from the CG v2 spec
  •  Example - Pharmacogenomics Pharmacogenomic Report Example instances
  •  Example - Full Bundle HLA genotyping for HLA-A, HLA-B, and HLA-C, using GLStrings Full Bundle HLA Typing Example
  •  Example - CYP2C19 report from 1000 Genomes CYP2C19 report from 1000 Genomes
  •  Example - subset of CYP2C19 report from 1000 Genomes showing phase Phase relation on CYP2C19 report
  •  Example - Multiple Oncology Variant Report Example Oncology Example Report with 12 reported variants
  •  Example - Melanoma implication Small example report with 1 reported variant and somatic diagnostic implication
  •  Example - Full Bundle Oncology Example Full Bundle Oncology Example
  •  Example - Complex Variant (HGVS) Compound Heterozygote Variant Example
  •  Example - Complex Variant (unpacked) Compound Heterozygote Variant example, using position, reference, and alternate allele instead of HGVS.
  •  Example - NGS SNV example
  •  Example - Variant with ACMG Screening ACMG annotated variant
  •  Example - High Risk Allele (HLA-B*15:02) High Risk Allele (HLA-B*15:02)
  •  Example - Inherited Disease Pathogenicity Inherited Disease Pathogenicity
  •  Example - HLA genotyping for HLA-A, HLA-B, and HLA-C, using GLStrings DiagnosticReport HLA Typing Example
  •  Example - HLA genotyping for HLA-A, using GLStrings HLA-A genoyping Example: HLA-A*03:01:01:01+HLA-A*30:01:01
  •  Example - Observation for a single HLA-A allele HLA-A allele observaation: HLA-A*03:01:01:01
  •  Example - Buccal swab for HLA typing Specimen example: Buccal swab for HLA typing
  •  Example - Service request for high-resolution HLA-A genotyping ServiceRequest example: High-resolution HLA-A genotyping

Code Systems

Code Systems defined in this implementation guide

  •  TBD Code System Code System for codes yet to be defined in LOINC
  •  Sequence Phase Relationship Code System for specific types of relationships

Value Sets

Value Sets defined in this implementation guide

  •  HGVS Value Set Value Set for HGVS
  •  HGNC Value Set Value Set for HGNC (genes and gene groups)
  •  TBD Value Set Value Set for codes yet to be defined in LOINC
  •  DNA Change Type DNA change type for variants
  •  Functional Annotations Functional annotations for variants
  •  Sequence Phase Relationship Value Set for specific types of relationships
  •  Variant Inheritance origins of variants

Concept Maps

Concept Maps defined in this implementation guide

  •  Concept mapping for DNA Change Type Mapping LOINC answers to SequenceOntology

Operations

Operations defined in this implementation guide

  •  Operation: $find-subject-variants Retrieves variants from a specified genomic region