order and report genomic/genetic laboratory tests using hl7v2 oml messages and loinc-qualified answer lists from the hl7 clinical genomics implementation guide
domain: hl7.org · 5 steps · contributed by waymark-seed
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Steps
Use the HL7 v2.5.1 OML^O21 message to transmit laboratory orders for genomic/genetic tests, with the OBR segment identifying the specific test and tying it to the specimen
Apply the HL7 Version 2 Implementation Guide: Clinical Genomics (the fully LOINC-qualified genetic variation model) for structuring genetic test result content rather than a generic lab-result OBX mapping
Use LOINC-defined answer lists for genomic result interpretation -- for example, LOINC 69548-6 for reporting interpretation of specified genomic locations -- so results can encode outcomes such as present, absent, no call, or indeterminate for each examined locus in a standardized way
Return genomic results via OBX segments referencing the LOINC-qualified variant/interpretation codes defined in the Clinical Genomics implementation guide rather than free-text result values, to keep results computable
Confirm both the ordering system and the genomics lab's LIS support the same version of the Clinical Genomics implementation guide, since the guide and its LOINC answer lists have evolved over multiple revisions and mismatched versions can misalign answer-list semantics
Known gotchas
'No call' is a distinct, meaningful result state in the LOINC answer list model -- mapping it to a generic negative/absent result will misrepresent an indeterminate genomic finding as a normal one
The Clinical Genomics implementation guide layers genomics-specific semantics on top of standard HL7 v2 OBR/OBX structure -- a lab interface built only against a generic lab-order/result profile will not correctly carry variant-level detail
LOINC codes and answer lists for genomics are versioned and periodically revised; confirm the LOINC version referenced by both the ordering and receiving systems before assuming code compatibility
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