Design

Warning

This document is a work in progress and is not ready for production use.

The eMERGE III electronic return of structured results project is motivated by several key design principles:

  1. All content in narrative report is structurally represented. All lab produced content from the narrative reports should be captured in structured forms so that it is possible to reconstruct the it.
  2. Codify concepts when reasonable. Drugs, diseases, genes, etc… should be codified based on FHIR and IG guidance. eMERGE concepts that extend beyond the FHIR and IG guidance should be codified if possible and within reason.
  3. Computationally Reliable representation of results TODO <add a general statement about aiming to achieve computationally useful representations, when possible>
  4. Reflect the composite nature of results Structure & codify both diagnostic primary/secondary disease pathogenicity interpretations and pharmacogenomic genotype finding medication implications.
  5. Representation of assay and case level gene coverage. Use text based assay definition, gene coverage and methodology description per lab. Include computational gene coverage report artifact if available.
  6. Attempt to enable Clinical Decision Support Support for computationally reliable sharing of short sequence variation, genotypes, diplotypes, large deletion/insertion/duplication (deferred CNVs).

Example Reports

The eMERGE reporting process is supported by two separate clinical workflows at the corresponding sequencing centers (SCs); The HGSC Lab at Baylor College of Medicine and The LMM Lab at Partners Healthcare (in conjunction with Broad Institute).

Below are two example (deidentified) positive reports one from each of the two SCs.

HGSC eMERGE Report
LMM eMERGE Report

Figure 1: HGSC & LMM eMERGE Report Examples (click to enlarge)

This section introduces the process used to convert and map these two similar reports into a common HL7 FHIR structure.

Report Layout & Structure

The subsections below show figures containing a general report model alongside an example report with all of the detailed elements mapped using coloring and numbered call outs. Each subsection represents one of the two SC report designs shown in the preceding section. This structuring and mapping exercise was thoroughly reviewed and vetted by users at each of the two SCs.

HGSC Report Structure

TODO <add a brief description of the common vs different elements from that of LMM>

The HGSC general report layout and detailed mapping to their example report…

HGSC eMERGE Report Layout
HGSC eMERGE Example Report Detailed Mapping

Figure 2: HGSC general report layout and detailed mapping (click to enlarge)

LMM Report Structure

TODO <add a brief description of the common vs different elements from that of HGSC>

The LMM general report layout and detailed mapping to their example report…

LMM eMERGE Report Layout
LMM eMERGE Example Report Detailed Mapping

Figure 3: LMM general report layout and detailed mapping (click to enlarge)

FHIR Report Schema & Resources

_images/schema-overview.png

Figure 4: FHIR Diagnostic Report Schema Alignment An illustration of the associations between the major report components and FHIR Diagnostic Report Schema.

FHIR Mapping

TODO <discuss the process for mapping CG IG profiles and FHIR resources to elements.>
<and mention the decision to follow the Genomics Reporting IG vs starting from scratch>

Genomics Reporting Guidance from IG

The eMERGE results FHIR is based on the Genomics Reporting profile and guidance from the FHIR Genomics Reporting Implementation Guide (STU1).

This specification aims to harmonize and leverage the draft work of the HL7 CG WG to both validate and inform its development. In cases where there are gaps or requirements that are unclear or unmet, they are raised with the HL7 CG WG and custom extensions or profiles are developed to fill the missing needs with the expectation that these issues will ultimately be reconcilable as the standard matures.

The table below lists the eMERGE report components and their preferred alignment based on the HL7 CG Genomics Reporting IG specification. For components that do not align cleanly alternative solutions are provided including but not limited to the introduction of custom extensions. The following section on Artifacts has a comprehensive catalogue of every resource, profile and extension used by this eMERGE specification.

No. Element FHIR Resource IG Profile/Ext Related Properties
1 Report DiagnosticReport Genomics Report
Test Disclaimer,
Gene Coverage
2 Patient Patient none  
3 Sample / Specimen Specimen Specimen Profile  
4 Request / Orderer ServiceRequest Service Request Profile  
5 Test Performed … PlanDefinition none
…Name,
…Background,
…Methodology,
…References
6
Ordering Provider,
Results Interpreter
PractitionerRole none  
7 Performing Lab Organization none  
8 Recommendations (Proposed) Task Recommended Followup  
9 Comments (Additional Notes) Observation none  
10 Overall Interpretation Observation Overall Interpretation Summary Text
11 Diagnostic Gene Panel Results Group Observation Grouper Summary Text
12 Clinical Interpretation Observation Inherited Disease Pathogenicity  
13 PGx Gene Panel Results Group Observation Grouper  
14 Medication Implication Observation  
15 Identified Variant Genotype Observation Variant  
16 Identified Variant Diplotype Observation Genotype  
X5 Summary Text none custom  
X6 Test Disclaimer none custom  
X7 Gene Coverage none Related Artifact Extension