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PEDIA-Charite / PEDIA-workflow

PEDIA-workflow prioritizes the disease-causing gene by integrating facial analysis and exome sequencing data.
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Check mutation status in json to case translation #25

Closed xiamaz closed 6 years ago

xiamaz commented 6 years ago

We are only interested in pathogenic mutations. Exclude benign mutations.

Currently all mutations are translated. Certainly benign mutations could be excluded prior to deeper hgvs analysis.

Implementation would be fairly straightforward, as only a minor check would need to be included in the hgvs variant generation in the case creation process. Depending on cutoff, all variants below our cutoff are excluded from the created variant.

Some issues remain:

Which cutoff for exclusion should we choose? (Uncertain, Pathogenic? How do we handle unlabeled mutations?)

xiamaz commented 6 years ago

Result cutoff

Currently provided result tags are:

ABNORMAL
ABNORMAL_DIAGNOSTIC
DELETION_DUPLICATION
NORMAL
NORMAL_FEMALE
NORMAL_MALE
NO_DELETION_DUPLICATION
NO_SIGNIFICANT_VARIANTS
VARIANTS_DETECTED

I will use these tags to denote benign results to be ignored from further processing:

NORMAL
NORMAL_MALE
NORMAL_FEMALE
NO_SIGNIFICANT_VARIANTS

I am not sure what NO_DELETION_DUPLICATION is supposed to mean and in which way we should interpret it. Unless we have reason to believe this to also denote benign results, I would ignore this one for now.

la60312 commented 6 years ago

Could you provide a report which contains the list of cases with these annotation? We have too many human operation in Face2Gene website, and the user sometime didn't update the case when they solved the case. We should check them case by case.