Artifacts

Figure 5 below illustrates a complete map of the resource, profile and extension FHIR artifacts used to support the eMERGE report defined by this specification. It starts at the center with #1 the GenomicsReport profile in purple from the FHIR CG Genomics Reporting IG. At the top are the red artifacts representing the patient and specimen concepts. The light green artifacts in the upper right hand side represent the order (Service-Request) and the ordered assay (PlanDefinition) along with the ordering and performing practitioners and their facility. The yellow artifacts on the left-hand side represent the top-level interpretation, comments and recommended actions, if applicable. The bottom half of the mapping diagram divides the diagnostic disease gene panel findings and results in pink on the left from the pharmacogenomic gene panel findings and results in green on the right. Both results and findings share common artifacts in orange at the bottom of the diagram to represent the variants and genotypes associated with the findings and results.

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Figure 5: Artifact Catalog Map A map of the associations between the major schema artifacts (resources, profiles and extensions).

The additional sub-diagrams at the bottom of Figure 5 contain the complete set of extensions utilized in this specification. These extensions were used from other sources when available as indicated or created as custom extensions if no reasonable alternative was available. These extensions primarily are used to extend the Patient (X1 thru X4) and GenomicsReport (X6 thru X8) concepts, but one extension was needed for capturing summary interpretation text (X5) on both the GenomicsReport and/or any Observation.

The following catalog provides a tabular view corresponding to the numbers in Figure 5 as well as the figures shown elsewhere in this specification. The links will open the specific artifact’s page in this specification.

No. Artifact FHIR Resource Description
1 Genomics-Report DiagnosticReport The top level resource representing the genetic test results report with the final findings and interpretations for the eMERGE Test Panel.
2 Patient Patient The patient for which the eMERGE Test Panel was ordered and fulfilled.
3 Specimen Specimen The sample or specimen collected from the patient being tested.
4 Service-Request ServiceRequest The fulfilled order for a patient along with the ordering practitioner, the specimen and the assay methodology and description performed.
5 (Assay) PlanDefinition PlanDefinition The plan definition resources is used to represent the eMERGE lab developed test (LDT) performed.
6 PractitionerRole PractitionerRole The practitioner role is used to represent the health care personnel in the context of their role and organization (e.g. geneticists, clinicians, etc..).
6a Practitioner Practitioner The practitioner is either the individual health care provider playing the role of an ordering physician or result interpreter when paired with the organization and practioner role.
7 Organization Organization The organization for the ordering provider, results interpreter and performing lab.
8 Recommended-Followup Task The recommended followup profile is a proposed task resource for structuring the return of recommendations for the report.
9 Report Comment Observation A generalized observation used by the performing lab to convey unstructured and uncoded comments about the report.
10 Overall-Interpretation Observation The overall interpretation for the diagnostic gene panel portion of the assay relative the primary indication for testing.
11 Dx Grouper Observation The grouping of diagnostic gene panel results to separate them from the PGx results and/or other logical groupings of results.
12 Inherited-Disease-Pathogenicity Observation The inherited disease pathogenicity interpretations for specific variant findings assessed in relation to the primary indication for testing which have the potential to also be secondary findings.
13 PGx Grouper Observation The grouping of PGx gene panel results to separate them from the diagnostic gene panel results.
14 Medication-Implication Observation The 3 types of medication implications: Metabolism, Efficacy, Transporter function interpretations used to assess PGx gene panel variant findings.
15 Variant Observation The variant profile supports the return of structured short sequence variants along with their zygosity for observed findings typically to support interpretations related to their clinical significance or in the context of the assay.
16 Genotype Observation The genotype profile supports the return of structured genotypes derived from individual variant alleles. This is used primarily to structure PGx diplotypes.
X# Extensions Extension The list of all extensions used throughout this specification with special emphasis on the few custom extensions developed by eMERGE to support the project’s requirements.