Clarification on comments re attribute geneticRegionOfInterest

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CLOSED - Need clarification on comments re attribute geneticRegionOfInterest (row 6)

Original Definition

For PerformedGeneticObservation.geneticRegionOfInterest

DEFINITION: The portion of the genome serving as a locus for the test, often a gene.

EXAMPLE(S): EGFR, KRAS, CYP2D6, MYC, MFNG

OTHER NAME(S):

NOTE(S): These are typically obtained from the gene symbol list maintained by the Human Genome Variation Society (HGVS). This can be a gene, a protein, or a sector as described by geneticRegionTypeCode.


NOTE: PerformedGeneticObservationResult.geneticRegionOfInterest has the same definition except it doesn’t have the last sentence in the NOTE(S) section.

Ballot Comment

HGNC is the international standard for gene symbols. HGVS is variant nomenclature.

Proposed Definition

DEFINITION: The portion of the genome serving as a locus for the test, often a gene.

EXAMPLE(S): EGFR, KRAS, CYP2D6, MYC, MFNG <= if we change the note, should we change the values here too?

OTHER NAME(S):

NOTE(S): HGNC gene symbols should be used.

Current Disposition

Pending Input From Submitter

Proposed Disposition Comment

Need to clarify if we should replace this with HGNC or just add HGNC to HGVS. Is the proposed wording prescribing a vocabulary binding? Also should run it by PGx SMEs?

Outstanding Questions

  • CDISC PGx SMEs: Is the proposed change consistent with the original use case for your concept?
  • Anyone: Should we replace existing note with the HGNC one (effectively prescribing a terminology binding) or just add the HGNC one as an alternative to HGVS?

Responses

Lauren Becnel: The gene symbols managed by HGNC can be annotated with variations, which are managed by HGVS and others.

Q from WENDY (TYPE: DISCUSS): Is this suggesting we change the note? Not sure what to make of this

DISCUSSION 20160225: Lauren’s response was to the outstanding question addressed to anyone re replacing the existing note with the HGNC one. Replace HGVS with HGNC in the note: "These are typically obtained from the gene symbol list maintained by the HUGO Genome Nomenclature Consortium (HGNC), a committee of the Human Genome Organization (HUGO). This can be a gene, a protein, or a sector as described by geneticRegionTypeCode."

UPDATE DONE IN THE MODEL


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