Discussion on PerformedGeneticObservationResult.mutationTypeCode

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Proposed New Definition and Examples for PerformedGeneticObservationResult.mutationTypeCode

Current Definition

DEFINITION: A coded value specifying whether a genetic variation is inheritable.

EXAMPLE(S): GERMLINE, SOMATIC

OTHER NAME(S):

NOTE(S):

Comment

This should be linked to the LOINC answer list with these values, which are more complete. Proposed wording: “Coded value defining the genomic source of the variant, which can indicate the variant context including inherited germline mutations, acquired tumor specific mutations, mutations within a fetus, or unknown origin.”

Proposed Disposition

Persuasive

Proposed Disposition Comment

Need to make sure this is consistent with PGx SME's understanding and we're not de-supporting their use case - also need to get official LOINC reference info. Are inherited germline mutations, acquired tumor specific mutations, mutations within a fetus, and unknown origin a broader set of example values we should use?

Initial Discussion

Concern was raised that this attribute name may be a misnomer; need to check with PGx SMEs re what was intended with this concept and what is the CDISC use case for it; concern was also raised about example values possibly conflating ideas; acknowledged that some members of CG WG have spent lots of time on this topic and could contribute; might be worth taking a look at ClinGen model, etc. to see how other models represent this concept – need to ensure it’s a model that includes both concepts (germline and somatic) otherwise it might not even have the concept

Outstanding Questions

• PGx SMEs: Does the following definition support your use case? Are the following examples valid?
  • DEFINITION: A coded value specifying the genomic source of the variant which can indicate the variant context.
  • EXAMPLE(S): inherited germline mutations, acquired tumor specific mutations, mutations within a fetus, and unknown origin
• Anyone: Are the original example values conflating ideas? What other models are there that include both germline and somatic mutations and how do they represent this idea?

Responses

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