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Automated HL7v2 LRI informatics framework for streamlining genomics-EHR data integration.

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Summary
This summary is machine-generated.

This study introduces a new tool to convert genomic data into HL7v2 LRI format, enabling structured data transfer from labs to Electronic Health Records (EHRs). This improves access to genetic variants and clinical annotations within EHR systems.

Keywords:
Clinical genomicsEHRElectronic health recordGenomics moduleHL7Laboratory informatics

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Area of Science:

  • Genomic data integration and health informatics.
  • Clinical bioinformatics and electronic health record (EHR) interoperability.

Background:

  • Next-generation sequencing data is commonly in VCF format, but most EHRs lack native VCF support, leading to unstructured PDF reports.
  • While FHIR adoption is growing, HL7 Version 2 (HL7v2) remains prevalent in EHR systems.
  • The HL7v2 Laboratory Results Interface (LRI) standard offers a framework for structured genomic data communication.

Purpose of the Study:

  • To extend an existing VCF to FHIR converter to generate HL7v2 LRI-compliant data, including variant annotations.
  • To implement an automated pipeline for transferring structured genomic data from clinical labs to EHRs.
  • To enhance data accessibility and utility of genomic information within EHR systems.

Main Methods:

  • Developed an open-source tool (hl7v2GenomicsExtractor) to convert genomic interpretation reports into HL7v2 observations conforming to HL7v2 LRI.
  • Extended the converter to support Epic's genomic import specification and alternative input formats.
  • Implemented an automated pipeline for direct data transfer into the EHR.

Main Results:

  • Successfully implemented an automated pipeline for moving structured genomic data from clinical labs to EHRs.
  • Genetic variant data and clinical annotations (phenotypes, therapeutic implications) are now viewable in EHRs via Epic's genomics module.
  • The converter successfully transformed genomic variant and clinical annotation data into HL7v2 messages for EHR integration.

Conclusions:

  • The developed HL7v2 converter enables structured, standards-based genomic data exchange between labs and EHRs.
  • This pipeline overcomes the limitations of static PDF reports, making genomic annotations calculable and structured within EHRs.
  • Addressing data variability in genomic interpretation reports was a key challenge during development and deployment.