vcf2fhir: a utility to convert VCF files into HL7 FHIR format for genomics-EHR integration
Abstract Background VCF 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...
| Main Authors: | , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2021-03-01
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| Series: | BMC Bioinformatics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12859-021-04039-1 |
| _version_ | 1818614950481887232 |
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| author | Robert H. Dolin Shaileshbhai R. Gothi Aziz Boxwala Bret S. E. Heale Ammar Husami James Jones Himanshu Khangar Shubham Londhe Frank Naeymi-Rad Soujanya Rao Barbara Rapchak James Shalaby Varun Suraj Ning Xie Srikar Chamala Gil Alterovitz |
| author_facet | Robert H. Dolin Shaileshbhai R. Gothi Aziz Boxwala Bret S. E. Heale Ammar Husami James Jones Himanshu Khangar Shubham Londhe Frank Naeymi-Rad Soujanya Rao Barbara Rapchak James Shalaby Varun Suraj Ning Xie Srikar Chamala Gil Alterovitz |
| author_sort | Robert H. Dolin |
| collection | DOAJ |
| description | Abstract Background VCF 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. Results vcf2fhir 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. Conclusions Experience 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. |
| first_indexed | 2024-12-16T16:26:09Z |
| format | Article |
| id | doaj.art-99d9ca08a72249798090ee08fc5ab9d3 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-16T16:26:09Z |
| publishDate | 2021-03-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-99d9ca08a72249798090ee08fc5ab9d32022-12-21T22:24:44ZengBMCBMC Bioinformatics1471-21052021-03-0122111110.1186/s12859-021-04039-1vcf2fhir: a utility to convert VCF files into HL7 FHIR format for genomics-EHR integrationRobert H. Dolin0Shaileshbhai R. Gothi1Aziz Boxwala2Bret S. E. Heale3Ammar Husami4James Jones5Himanshu Khangar6Shubham Londhe7Frank Naeymi-Rad8Soujanya Rao9Barbara Rapchak10James Shalaby11Varun Suraj12Ning Xie13Srikar Chamala14Gil Alterovitz15Elimu InformaticsDepartment of Pathology, Immunology and Laboratory Medicine, University of FloridaElimu InformaticsIntermountain HealthcareDivision of Human Genetics, Cincinnati Children’s Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of MedicineComputational Health Informatics Program, Boston Children’s HospitalElimu InformaticsElimu InformaticsLeap of FaithElimu InformaticsElimu InformaticsElimu InformaticsLexington High SchoolBiomedical Cybernetics Laboratory, Department of Medicine, Brigham and Women’s HospitalDepartment of Pathology, Immunology and Laboratory Medicine, University of FloridaBrigham and Women’s HospitalAbstract Background VCF 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. Results vcf2fhir 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. Conclusions Experience 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.https://doi.org/10.1186/s12859-021-04039-1FHIRClinical genomicsSMART-on-FHIREHR integrationNext-generation sequencing |
| spellingShingle | Robert H. Dolin Shaileshbhai R. Gothi Aziz Boxwala Bret S. E. Heale Ammar Husami James Jones Himanshu Khangar Shubham Londhe Frank Naeymi-Rad Soujanya Rao Barbara Rapchak James Shalaby Varun Suraj Ning Xie Srikar Chamala Gil Alterovitz vcf2fhir: a utility to convert VCF files into HL7 FHIR format for genomics-EHR integration BMC Bioinformatics FHIR Clinical genomics SMART-on-FHIR EHR integration Next-generation sequencing |
| title | vcf2fhir: a utility to convert VCF files into HL7 FHIR format for genomics-EHR integration |
| title_full | vcf2fhir: a utility to convert VCF files into HL7 FHIR format for genomics-EHR integration |
| title_fullStr | vcf2fhir: a utility to convert VCF files into HL7 FHIR format for genomics-EHR integration |
| title_full_unstemmed | vcf2fhir: a utility to convert VCF files into HL7 FHIR format for genomics-EHR integration |
| title_short | vcf2fhir: a utility to convert VCF files into HL7 FHIR format for genomics-EHR integration |
| title_sort | vcf2fhir a utility to convert vcf files into hl7 fhir format for genomics ehr integration |
| topic | FHIR Clinical genomics SMART-on-FHIR EHR integration Next-generation sequencing |
| url | https://doi.org/10.1186/s12859-021-04039-1 |
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