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Additions to guide pages
New guide page (detailing criteria for "sufficiently evaluated"). Also, added guideline against pooling data to achieve greater statistical significant with case/control data.
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|+$gOut["title"] = "GET-Evidence: Sufficiently vs. Insufficiently Evaluated Classification";|
|+$gOut["content"] = $gTheTextile->textileThis (<<<EOF|
|+h1. Sufficiently vs. Insufficiently Evaluated Classification|
|+Variants in GET-Evidence will not be listed in the main part of a genome report unless they are considered "sufficiently evaluated". Otherwise, they are listed in the "insufficiently evaluated" variants report, sorted by prioritization score.|
|+For a variant to be sufficiently evaluated, it needs to have "variant impact scores":guide_impact_score evaluated such that it can be automatically ranked in the genome report.|
|+h2. Criteria for "Sufficiently Evaluated"|
|+h3. Variant evidence scores|
|+At least one of either *"Case/control"* OR *"Familial"* scores must be recorded.|
|+Note that a score of zero is acceptable (i.e. if there is no significant evidence in the category). For example, a variant only once observed in a single child -- lacking both case/control and familial segregation data -- could score zero points in both categories.|
|+h3. Clinical impact scores|
|+For "benign" variants, no scores need to be recorded for this section.|
|+For other variants, both *"Severity"* AND *"Penetrance"* must be recorded.|