eMERGE Results FHIR Specification

Warning

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

Introduction

This is the eMERGE Phase III specification detailing the design for generating structured genetic test lab results using HL7 FHIR Genomics Reporting Implementation Guidelines.

Below you can find background information on eMERGE Phase III Results, eMERGE Pilot Implementation, and Specification Aim.

How to read this Guide

This Guide is divided into several pages which are listed at the top of each page in the menu bar.

  • Home: The home page provides the introduction and background for the eMERGE Results FHIR Specification.

  • Design: These pages provide insights into the process used to generate the specification.

    • Example Reports: This section provides examples of the 2 different versions of lab reports used during eMERGE III.
    • Report Layout & Structure: This section describes how the 2 different report versions were generalized and mapped into common components.
    • FHIR Report Resources: This section introduces the FHIR Diagnostic Report and associated sub component resources relevant to the eMERGE report model.
  • Artifacts: … (catalogue of artifacts & detailed pages)

    • Catalogue (classified as core, ig, custom) (table of resources)
    • Custom Extensions (3)
  • Issues & Resolutions: This section contains a comprehensive listing of issues in mapping and structuring the eMERGE data to the Genomics Reporting IG (STU1) and their resolutions.

  • Discussion: This section contains discussions on strategic concerns with adoption, concerns related to representing variation and potential future use cases.

  • Supplemental Material: … (presentation, paper, github, definitions spreadsheet, examples, etc…)

FHIR Genomics Reporting IG

This specification in built on top of the FHIR Genomics Reporting Implementation Guide (STU1) which is under active development by the HL7 Clinical Genomics WG. During the development of this specification the FHIR Genomics Reporting Implementation Guide (STU1) progressed from Draft to Standard for Trial Use version 1.

eMERGE Phase III Results

The eMERGE Results HL7 FHIR Specification is a product of the eMERGE network and was initiated by the EHR Integration Workgroup during phase III of the study. It focuses on providing an HL7 FHIR electronic message standard for returning the lab results for the eMERGEseq Platform panel assays performed by the two eMERGE Sequencing Centers (SC) for the individual eMERGE sites. During the fulfillment of the eMERGESeq Platform of phase III an XML schema was specified and all results were generated, delivered and stored using this format. This specification is an evolution of the phase III eMERGE XML structure Schema.

eMERGE Pilot Implementation

eMERGE is piloting and implementation of this specification in conjunction with its development and release which includes a subset of the eMERGEseq Platform’s panel results returned from the SCs.

Specification Aim

The aim of the eMERGE test results return specification and implementation is to inform the efforts of the HL7 CG workgroup so as to accelerate the process towards a normative standard for general practice in clinical genetic test reporting.