GenomeX Data Exchange FHIR IG
0.2.0 - draft

GenomeX Data Exchange FHIR IG, published by MITRE. This guide is not an authorized publication; it is the continuous build for version 0.2.0 built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/CodeX-HL7-FHIR-Accelerator/GenomeX-DataExchange/ and changes regularly. See the Directory of published versions

Transport Messaging

GenomeX data transport for genomic lab orders and results.

This GenomeX IG describes FHIR resources for genomic test results with the goal of enabling precision medicine workflows. However, the FHIR resource content described in this IG only describes the results from genomic lab. Integration of order placement is also required to scale genomic lab testing.

This supplemental content is intended to frame the transport options when blending HL7v2 ordering with FHIR results to complete the request/reply exchange between order placers (HCO/EHR) and order fillers (Lab). The options presented here assume HL7v2 ORM/ORU message exchange is a baseline capability offered by most EHR vendors and Labs.

This supplemental content guide is intended to describe an HL7v2 to FHIR transition architecture.

The content presented under each scenario header below describes the data and transport relationships between the HL7 ORM/ORU messages and the GenomeX FHIR bundle.

  1. Order via HL7v2 ORM & GenomeX FHIR bundle base64 encoded via HL7v2 ORU
  2. Order via HL7v2 ORM & GenomeX FHIR bundle download via FHIR API URL embedded in the HL7v2 ORU
  3. Order via HL7v2 ORM & GenomeX FHIR bundle download via FHIR API polling

FHIR servers are recommended to adopt SMART on FHIR with asymmetric key profile. SMART on FHIR is an HL7 standard widely supported in healthcare.

Order via HL7v2 ORM & GenomeX FHIR bundle base64 encoded in HL7v2 ORU

Steps:

  • EHR system places a new order through HL7 ORM into lab
  • Lab sends Observation Result (ORU) with a FHIR bundle as base64 string embedded in an OBX segment

HL7v2 ORU would contain report bundle as a base64 string in the OBX segment

  • OBX-2 = ED (Encapsulated Data)
  • OBX-5 = Base 64 string
MSH|^~\&|<Sending Application>|<Sending Facility>|<Receiving Application>|<Receiving Facility>|20240104093000||ORU^R01|12345678910|T|2.5.1
PID|1||123456789||Last^First||19450912|M|||123 Fake St.^^Chicago^IL^60614
OBR|1|12345678|24abcdef|GTEST^Sample Test1|||20240101|||||||||0123456789^TEST^CLINICIAN^^^^^^^^^^NPI
OBX|1|ED|GENOMEXBUNDLE^Genome X Bundle^TMPLRR||^^PDF^Base64^<Base64 GenomeX bundle>|

Order via HL7v2 ORM & GenomeX FHIR bundle download via FHIR API URL embedded in the HL7v2 ORU

Steps:

  • EHR system places a new order through HL7 ORM into lab
  • Lab sends Observation Result (ORU) with an HTTP link to FHIR server in an OBX segment
  • EHR receives HL7 and issues a HTTPs GET request to the FHIR server for the report
  • FHIR server returns a report as an HTTPs response

HL7v2 ORU will contain a reference pointer to FHIR source.

  • OBX-2 = RP (Reference Pointer)
  • OBX-5 = URL to FHIR resource

Additionally, LOINC code 81247-9^Master HL7 genetic variant reporting panel^LN should be used.

MSH|^~\&|<Sending Application>|<Sending Facility>|<Receiving Application>|<Receiving Facility>|20240104093000||ORU^R01|12345678910|T|2.5.1
PID|1||123456789||Last^First||19450912|M|||123 Fake St.^^Chicago^IL^60614
OBR|1|12345678|24abcdef|GTEST^Sample Test1|||20240101|||||||||0123456789^TEST^CLINICIAN^^^^^^^^^^NPI
OBX|1|RP|81247-9^Master HL7 genetic variant reporting panel^LN||<FHIR Server HTTPS URL>|||||F

Order via HL7v2 ORM & GenomeX FHIR bundle download via FHIR API polling

Steps:

  • EHR system places a new order through HL7 ORM into lab
  • EHR polls periodically and searches for any reports available for order placed, using search parameters in the FHIR servers search endpoint
  • EHR issues a HTTP GET request to the FHIR server for the report/bundle
  • Lab FHIR server returns GenomeX report/bundle as a HTTP response