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. 2022 May 23:2022:236-243.
eCollection 2022.

Applying FHIR Genomics for Research - From Sequencing to Database

Sean Hernandez  1 , Karen Fairchild  2   3 , Mark Pemberton  4 , Jonathan Dahmer  2 , Wei Zhang  1 , Matvey B Palchuk  2 , Umit Topaloglu  1
Affiliations

Applying FHIR Genomics for Research - From Sequencing to Database

Sean Hernandez et al. AMIA Jt Summits Transl Sci Proc. .

Abstract

The availability of next-generation sequencing (NGS) technologies and their continually declining costs have resulted in the accumulation of large genomic data sets. NGS results have traditionally been delivered in PDF format, and in some cases, structured data, e.g., XML or JSON formats, are also made available, but there is a lack of uniformity around the profiling of external vendor testing platforms. Atrium Health Wake Forest Baptist and TriNetX have harmonized and mapped genomic data to FHIR Genomic standards and imported it into the TriNetX database through a data pipeline. This process is translatable to other sequencing platforms and to other institutions. The addition of genotypic data to the TriNetX database to the reservoir of phenotypic data will promote enhanced industry trial recruitment, (ii) comprehensive intra-institutional genomic benchmarking/quality improvement, and eventually (iii) sweeping inter-institutional genomic research and treatment paradigm shifts.

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Figures

Figure 1.
Figure 1.
Atrium Health Wake Forest Baptist NGS result pipeline from major vendors.
Figure 2.
Figure 2.
HL7 FHIR MolecularSequence Resource model
Figure 3.
Figure 3.
Variant Profile (http://hl7.org/fhir/uv/genomics-reporting/STU1/variant.html)
Figure 4.
Figure 4.
LOINC Codes used in WF Codeable Concepts (full list located at https://loinc.org/81247-9/)
Figure 5.
Figure 5.
The data pipeline to the TriNetX database.
Figure 6.
Figure 6.
This is a use-case utilizing the data visual software provided by TriNetX with phenotypic and genotypic criteria selected from our institution’s pool of patients.
See this image and copyright information in PMC

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