add/edit evidence help text needs some updating

[jmcmichael]

Clinical Significance should mention the new Oncogenic evidence type

Positive or negative association of the Variant with predictive, prognostic, diagnostic, or predisposing evidence types. If the variant was not associated with a positive or negative outcome, N/A should be selected. Evidence Type must be selected before this field is enabled.

There was also some discussion in the meeting about clarifying N/A options for field combinations where that will be the only option provided.

[susannasiebert]

It also needs to mention Functional. Predisposing needs to be removed from the first sentence. Oncogenic and Predisposing need a sentence explaining that only NA applies.

[malachig]

Proposed new text for a few places:

Beside Clinical Significance: The impact or consequence of the variant evidence for predictive, prognostic, diagnostic, or functional evidence types. Evidence Type must be selected before this field is enabled. For predisposing and oncogenic evidence, impact is only applied at the assertion level and N/A should be selected here.

Below Evidence Type when Predisposing is selected: Evidence pertains to a germline variant's role in conferring susceptibility to a disease. Follow the ACMG guidelines for variant pathogenicity when evaluating evidence of this type.

Below Evidence Type when Oncogenic is selected: Evidence pertains to a somatic variant that induces or increases oncogenic cellular potential (pathogenicity in cancer context). Follow the Standard Operating Procedure for the Interpretation of Oncogenicity of Somatic Variants when evaluating evidence of this type.

Beside Evidence Direction: An indicator of whether the evidence statement supports or refutes the clinical significance of an event. Evidence Type must be selected before this field is enabled. Not applicable to Predisposing and Oncogenic evidence where directionality is incorporated in to pathogenicity/oncogenicity classifications assigned at the assertion level.

[malachig]

Consensus update from our group discussion (Obi, Malachi, Jason, Lana, Arpad, KK) this morning:

Beside Clinical Significance:

The impact of the variant for predictive, prognostic, diagnostic, or functional evidence types. For predisposing and oncogenic evidence, impact is only applied at the assertion level and N/A should be selected here.

Below Evidence Type when Predisposing is selected: Evidence pertains to a germline variant's role in conferring susceptibility to disease (including pathogenicity evaluations).

Below Evidence Type when Oncogenic is selected: Evidence pertains to a somatic variant’s involvement in tumor pathogenesis as described by the Hallmarks of Cancer.

Beside Evidence Direction: An indicator of whether the evidence statement supports or refutes the clinical significance of an event. For predisposing and oncogenic evidence, directionality is only applied at the assertion level and N/A should be selected here.

[obigriffith]

These edits have now been pushed to staging.

[lsheta]

We should consider modifying the text beside Evidence Statement:

Currently, it only refers to predictive, diagnostic and prognostic evidence.

Your original description of evidence from published medical literature detailing the association of or lack of association of a variant with diagnostic, prognostic or predictive value in relation to a specific disease (and treatment for predictive evidence). Data constituting protected health information (PHI) should not be entered. Please familiarize yourself with your jurisdiction's definition of PHI before contributing.

[lsheta]

If CIViC is supported by American funding sources, should curators be expected to familiarize themselves with U.S. definitions of PHI?

My understanding is that the specific concept of PHI is a HIPPA product, which makes it somewhat U.S. specific, too.

If a curator is working from a country where there's no regulation of PHI, and they submit a patients full name, we would still report it, although the curator's jurisdiction would not have an issue with it.

Tangentially related: Do we want oncogenic before functional in the select Type menu, or does it not really matter?

[lsheta]

How about

Your original description of evidence from published literature detailing the association or lack of association between a variant and its predictive, prognostic, diagnostic, predisposing, functional or oncogenic value. Data constituting protected health information (PHI) should not be entered. Please familiarize yourself with the U.S. definition of PHI before contributing.

[malachig]

Your original description of evidence from published literature detailing the association or lack of association between a variant and its predictive, prognostic, diagnostic, predisposing, functional or oncogenic value. Data constituting personal or identifying information should not be entered (e.g. protected health information (PHI) as defined by HIPAA in the U.S. and/or comparable laws in your jurisdiction).