How is the isDeleterious column in the CCLE_mutations.csv file determined?

I am curious to know how TRUE/FALSE is determined in the isDeleterious column of the CCLE_mutations.csv file. Is it a combined score of multiple variant predictors? Apologies, if this is already written up in a publication.

The isDeleterious is an outdated annotation which we do not recommend using. We will drop this in a future release. Please use the column ā€˜Variant_annotationā€™ instead.

Thanks for getting back to me @jnoorbak, are there plans to include a SIFT/PolyPhen scores to these mutations? Perhaps this was the original intent of isDeleterious?

The original goal has been somewhat to get the damaging effect of the mutation. This column in most cases corresponds to one of the following mutation types from ā€˜Variant_Classificationā€™ column (Oncotator annotations), but there are exceptions to that:

ā€˜De_novo_Start_OutOfFrameā€™, ā€˜Nonsense_Mutationā€™, ā€˜Nonstop_Mutationā€™, ā€˜Splice_Siteā€™, ā€˜Frame_Shift_Delā€™, ā€˜Frame_Shift_Insā€™, ā€˜Start_Codon_Delā€™, ā€˜Start_Codon_Insā€™, ā€˜Stop_Codon_Delā€™, ā€˜Stop_Codon_Insā€™

We do have a plan to update the mutation functional annotations in the future, but its timeline is unclear right now. We do generate SIFT/PolyPhen scores that are not reported right now. Iā€™ll keep in mind including them once we get to that. -Thanks

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Thank you for the clarification, I will mark your response here as the solution.

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