Build a FHIR Genomics Reporting IG diagnostic report with MolecularSequence for clinical genomics

In-depth guide

Steps

1. Create a GenomicsReport DiagnosticReport (profile: genomics-report from hl7.fhir.uv.genomics-reporting); set DiagnosticReport.code to LOINC 81247-9 ('Master HL7 genetic variant reporting panel') or another appropriate panel code
2. Populate DiagnosticReport.performer with the genetic testing laboratory and DiagnosticReport.specimen with the Specimen resource describing the sample (blood, tumor biopsy, saliva)
3. Create MolecularSequence resources to capture raw sequencing context: set MolecularSequence.type to 'dna', 'rna', or 'aa'; populate the referenceSeq element with the reference genome build (e.g., GRCh38) and chromosome information
4. Create Variant Observation resources (profile: variant from the Genomics Reporting IG) for each identified variant; link them to MolecularSequence via Observation.derivedFrom if the variant was detected from that sequence
5. Add DiagnosticImplication Observation resources (profile: diagnostic-implication) to record clinical significance, predicted impact, and associated condition using the appropriate value sets from the Genomics Reporting IG
6. Assemble all Variant, DiagnosticImplication, and MolecularSequence references into DiagnosticReport.result; set DiagnosticReport.status to 'final' upon completion