ArticleBMC bioinformatics2021
vcf2fhir: a utility to convert VCF files into HL7 FHIR format for genomics-EHR integration.
Article in BMC bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Genetic data normalization for genomic medicine: a Fast Healthcare Interoperability Resources Genomics reference implementation.Journal of the American Medical Informatics Association : JAMIA · 2025Article
- Genomics on FHIR - a feasibility study to support a National Strategy for Genomic Medicine.NPJ genomic medicine · 2025Article
- Sync for Genes Phase 5: Computable artifacts for sharing dynamically annotated FHIR-formatted genomic variants.Learning health systems · 2023Article
- Machine Learning-Enabled Clinical Information Systems Using Fast Healthcare Interoperability Resources Data Standards: Scoping Review.JMIR medical informatics · 2023Article
- Designing Interoperable Health Care Services Based on Fast Healthcare Interoperability Resources: Literature Review.JMIR medical informatics · 2023Review
- Introducing HL7 FHIR Genomics Operations: a developer-friendly approach to genomics-EHR integration.Journal of the American Medical Informatics Association : JAMIA · 2023Article
- Automated HL7v2 LRI informatics framework for streamlining genomics-EHR data integration.Journal of pathology informatics · 2023Article
- HL7 FHIR-based tools and initiatives to support clinical research: a scoping review.Journal of the American Medical Informatics Association : JAMIA · 2022Article
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Authors and funding
16 authors.
Funding
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Abstract
backgroundVCF formatted files are the lingua franca of next-generation sequencing, whereas HL7 FHIR is emerging as a standard language for electronic health record interoperability. A growing number of FHIR-based clinical genomics applications are emerging. Here, we describe an open source utility for converting variants from VCF format into HL7 FHIR format.
resultsvcf2fhir converts VCF variants into a FHIR Genomics Diagnostic Report. Conversion translates each VCF row into a corresponding FHIR-formatted variant in the generated report. In scope are simple variants (SNVs, MNVs, Indels), along with zygosity and phase relationships, for autosomes, sex chromosomes, and mitochondrial DNA. Input parameters include VCF file and genome build ('GRCh37' or 'GRCh38'); and optionally a conversion region that indicates the region(s) to convert, a studied region that lists genomic regions studied by the lab, and a non-callable region that lists studied regions deemed uncallable by the lab. Conversion can be limited to a subset of VCF by supplying genomic coordinates of the conversion region(s). If studied and non-callable regions are also supplied, the output FHIR report will include 'region-studied' observations that detail which portions of the conversion region were studied, and of those studied regions, which portions were deemed uncallable. We illustrate the vcf2fhir utility via two case studies. The first, 'SMART Cancer Navigator', is a web application that offers clinical decision support by linking patient EHR information to cancerous gene variants. The second, 'Precision Genomics Integration Platform', intersects a patient's FHIR-formatted clinical and genomic data with knowledge bases in order to provide on-demand delivery of contextually relevant genomic findings and recommendations to the EHR.
conclusionsExperience to date shows that the vcf2fhir utility can be effectively woven into clinically useful genomic-EHR integration pipelines. Additional testing will be a critical step towards the clinical validation of this utility, enabling it to be integrated in a variety of real world data flow scenarios. For now, we propose the use of this utility primarily to accelerate FHIR Genomics understanding and to facilitate experimentation with further integration of genomics data into the EHR.
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