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

Q&A
1

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.

2

The isDeleterious is an outdated annotation which we do not recommend using.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.

3

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?

4

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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5

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

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