update oncogenicity proposition to current va-spec model #219
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ahwagner
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Nov 17, 2024
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| variantOriginQualifier: | ||
| type: string | ||
| description: >- | ||
| Reports whether the proposition should be interpreted in the context of an inherited | ||
| (germline) variant, an acquired (somatic) mutation, or both (combined). | ||
| enum: | ||
| - germline | ||
| - somatic | ||
| - combined | ||
| allelePrevalenceQualifier: | ||
| Reports whether the proposition should be interpreted in the context of a heritable | ||
| (germline) variant, an acquired (somatic) mutation, or more nuanced origin. | ||
| $ref: "/ga4gh/schema/gks-core/1.x/json/MappableConcept" |
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@larrybabb note that some of our qualifiers had enums, where I am now updating them to MappableConcept. This is useful because even though some things seem obvious now (e.g. germline/somatic/combined for allele origin), there may be a desire in communities for more nuanced concepts (e.g. somatic mosaicism for allele origin) and not constraining to enums allows us to keep these fields broadly useful and reusable across current and future implementations and guidelines.
| @@ -1035,7 +1027,7 @@ $defs: | |||
| maturity: draft | |||
| type: object | |||
| description: >- | |||
| A proposition describing the role of a variant in causing an inherited condition. | |||
| A proposition describing the role of a variant in causing a heritable condition. | |||
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Note the slight difference between "inherited" and "heritable" here. de novo variants, for example, are heritable (and interpretable by ACMG guidelines) but not inherited.
larrybabb
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Nov 19, 2024
* gks-tech sync prep: reorg core/va classes and get tests working * changes from 2024-11-13 gks-tech sync review * gks-tech-updates from 11-15-2024 mtg * final change before 11/15/24 sync meeting * DRY refactor SubjectVariant in propositions * evidence code enum revision (#218) * update oncogenicity proposition to current va-spec model (#219) * init trial use coverage tests * revise available attributes in base models * bring test examples in line with schema changes * add coverage exception config --------- Co-authored-by: Alex H. Wagner, PhD <Alex.Wagner@nationwidechildrens.org>
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@larrybabb I plan to merge this into our update branch, but separating this PR out to highlight some changes we might consider making to pathogenicity propositions before going to Trial Use.