ga4gh / ga4gh/phenopacket-schema
Support variant representation and interpretation outside of a Disease context (e.g., PGx)
- Dominant language
- Java
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- 101
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Description
## Background
We need to describe variants of interest that exist outside the context of a specific disease diagnosis. For example, a Pharmacogenomic (PGx) variant may have significant clinical utility but lack any associated phenotypic manifestation.
Right now, the schema forces users to provide an interpretation of a variant strictly within the context of a `Case`, and a case is always evaluated in light of a `Diagnosis`. Placing a non-pathogenic PGx interpretation inside a "diagnosis" block is structurally awkward and semantically incorrect.
In addition, the progress status for interpretations relies on terminology (e.g., "completed", "solved/unsolved") that is heavily focused on Mendelian or rare disease diagnostic odysseys searching for novel genes. This terminology does not translate well to standard clinical environments where a PGx test is simply a routine screening.
## Proposed solutions for discussion
- Decouple variant interpretation from the strict `Diagnosis`/`Case` hierarchy.
- Investigate if PGx and non-disease variant data would be better positioned within the hierarchy alongside `Measurements`.
- Refactor the progress status terminology to support broader clinical and preventive genomics workflows.
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