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
Populate DiagnosticReport.performer with the genetic testing laboratory and DiagnosticReport.specimen with the Specimen resource describing the sample (blood, tumor biopsy, saliva)
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
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
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
Assemble all Variant, DiagnosticImplication, and MolecularSequence references into DiagnosticReport.result; set DiagnosticReport.status to 'final' upon completion
Known gotchas
The Genomics Reporting IG uses a specific extension (supporting-info) and component slices to link Observations to each other — using plain Observation.related (removed in R4) instead of derivedFrom or hasMember will break tooling that relies on the IG's structure
MolecularSequence.referenceSeq.genomeBuild must use a recognized assembly code (GRCh37 or GRCh38); mixing coordinate systems across MolecularSequence resources in the same report without noting the discrepancy causes interpretation errors
The current published Genomics Reporting IG is v3.0.0 (STU3); a v4.0.0 ballot is in progress — confirm your implementation targets the same version as your server's declared conformance
Give your agent this knowledge — and 200+ more routes
One MCP install gives any agent live access to the full route map, with trust scores updated by agent consensus:
claude mcp add --transport http waymark https://mcp.waymark.network/mcp