Genomics Reporting Implementation Guide
3.0.1-SNAPSHOT - Ballot 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 3.0.1-SNAPSHOT built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of and changes regularly. See the Directory of published versions

Somatic Reporting

This section deals with reporting observations related to cancer genomics. This includes reporting variants found in a tumor specimen, germ-line variants with known links to somatic events such as increasing risk for developing particular cancers, molecular biomarker observations that affect cancer care, and more. Beyond reporting variants and biomarkers, we also provide "implication" profiles to communicate observed links between variants and relevant knowledge bases such as professional guidelines and publications, for diagnostic and therapeutic implications, for predicted oncogenicity, etc. This sort of reporting is particularly prominent when dealing with cancer-related specimens, but can also include transplanted tissue and other forms of mosaicism.

General guidance

At the heart of a typical somatic report are findings (variants, haplotypes, genotypes, biomarkers) and annotations derived from those findings (diagnostic implications, therapeutic implications, predicted molecular consequences), as shown in the following figure:


These constructs are assembled within the broader context of the Genomics Report, which generally contains information about the specimen(s) and providers and organizations involved in the ordering and testing process. The report may also contain details about the genomic study analyses used to obtain the findings, as shown in the following figure:

Somatic report overview

Building a Somatic Report: An Example

This section provides a walk-through of mapping from an example somatic report to FHIR using the structure definitions and guidance defined in this IG. A somatic report focuses on the implications of a patient’s genetics (generally the therapeutic implications of somatic variants). The somatic report is represented as a Genomics Report. The related observations and other resources are referenced by the report. The intention of this section is to provide a “User Guide”, based on a specific report example, highlighting how the defined profiles can be used together to encode important relations in somatic reporting.

The following four images are pages 1-4 of a synthetic somatic report that is designed to illustrate a wide range of findings and implications.

report page 1report page 2
report page 3report page 4

Example FHIR Genomics instances

The somatic GenomicsReport which connects to all the FHIR Genomics instances for this detailed somatic example is here. A mapping spreadsheet is provided here. Alternatively, look in the table below for just those profiles of interest.

Label Resource / Profile Example(s)
9Diagnostic ImplicationNOTCH1-significance, ZFHX3-significance, MSH2-del-disease, NTHL1-snv-disease, STAG2-insertion-significance, ATR-insertion-significance, EGFR-L858R-significance, ROS1-Fusion-disease
14Genomic StudysomaticStudy
14Genomic Study AnalysisanalysisTumorNormalDNA, analysisTumorRNA
14Genomics Data FileWES-UncallableRegions-GRCh38 (BED file), somaticVCFfile (VCF file), FullGenome-GRCh38 (BED file)
1Genomics ReportsomaticReport
13HaplotypeHLA-A-haplotype1, HLA-A-haplotype2, HLA-B-haplotype1, HLA-B-haplotype2, HLA-C-haplotype1, HLA-C-haplotype2
12Molecular BiomarkerTMBExample, MSIExample, PDL1Example
11Molecular ConsequencesNOTCH1-uncertain-molc, ZFHX3-uncertain-molc, MSH2-del-molc, NTHL1-snv-molc, STAG2-insertion-molc, ATR-insertion-molc, EGFR-L858R-molc, ROS1-Fusion
6PractitionerorderingPractitioner, pathologistPractitioner, supervisorPractitioner
4Service RequestsomaticServiceRequest
3SpecimentumorSpecimen, normalSpecimen
10Therapeutic ImplicationROS1-Fusion-therapuTrial, ROS1-Fusion-therapuDrug, EGFR-L858R-therapuDrug1, EGFR-L858R-therapuDrug2, TMB-therapuDrug
8VariantNOTCH1-uncertain-var, ZFHX3-uncertain-var, MSH2-del-var, NTHL1-snv-var, STAG2-insertion-var, ATR-insertion-var, EGFR-L858R-var, ROS1-Fusion-var

Additional somatic-specific examples

  • Full transaction bundle containing a Genomics DiagnosticReport referencing, Patient, Practitioner, Specimen, with Tumor Mutational Burden and MSI Status Observations, Variant Observations for JAK2/KDR/ERBB4 SNV analyses, and 4 derived Therapeutic Implication Observations.
  • Multiple Oncology Variant Report Example Oncology Example Report with 12 reported somatic variants
  • Melanoma implication Small example report with 1 reported variant and diagnostic implication.