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Specification:

Genomics Reporting (FHIR)
Raised in Version:

1.0 [deprecated]
Work Group:

Clinical Genomics
Related Page(s):

genomics [deprecated]
Resolution Description:
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create an illustrative example of sequence phase relation using our defined list http://build.fhir.org/ig/HL7/genomics-reporting/ValueSet-seq-phase-relationship.html

remove old list from glossary + documentation, point out that we don't use the example list on the code.

reach out to LOINC to request a corresponding new answer list to https://loinc.org/82120-7/ for allelic phase.
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create an illustrative example of sequence phase relation using our defined list http://build.fhir.org/ig/HL7/genomics-reporting/ValueSet-seq-phase-relationship.html remove old list from glossary + documentation, point out that we don't use the example list on the code. reach out to LOINC to request a corresponding new answer list to https://loinc.org/82120-7/ for allelic phase.
Resolution Vote:
Jamie Jones / Bob Freimuth : 7 - 0 - 0
Change Category:
Clarification
Change Impact:
Non-substantive

Sequence Phase Relationship http://build.fhir.org/ig/HL7/genomics-reporting/StructureDefinition-sequence-phase-relationship.html
Indicates whether two entities are in Cis (same strand) or Trans (opposite strand) relationship to each other; however, the concept is linked to the LOINC: https://loinc.org/82120-7/ which has a different answer list attached.

The suggested answer list override in the FHIR documentation is not obvious and could result in misuse and confusion. The fact that there is a conflicting answer list suggested from what the LOINC has documented should be called out much more clearly.
The LOINC answer list for Allele Phase (82120-7) should be replaced with an answer list which includes the values "cis", "trans", and "unknown" (at least). The current answer list depicts allele inheritance, not allele phase, and uses confusing verbiage to try and represent variants in the same allele based on sequence data.