Possible To Annotate Insertions/Deletions In Mutationassessor?

Question

[Nick Khaz]

I was wondering if anyone has experience annotating mutations with MutationAssessor, and could comment on whether the tool can handle insertion and deletion events in addition to simple SNPs.

For example, using http://mutationassessor.org/v1/ If I wanted to look for a simple SNP I could enter

1, 100122272, G, A

and get a sensible annotation. But what if I had a deletion? It doesn't seem that MutationAssessor can handle something like:

1, 100122272, G,-

or

1, 100122272, G,*

or

1, 100122272, GA,G

I noticed the recent TCGA Ovarian paper (10.1038/nature10166) provides some supplementary info listing mutations supposedly annotated using MutationAssessor. These includes INS/DEL events. However, I haven't been able to find any documentation on whether MutationAssessor handles such mutations, or if there is a way to input such mutation events into the web tool.

Thanks.

Answer 1

[B. Arman Aksoy]

Because of the way MutationAssessor calculates the deleterious effect of a variant, it only works for missense events and not for in-dels; this is simply due to the fact that there is no really good way of looking at the cross-species aggregated conservation of a region that has an in-del event associated with it.

The TCGA MAF files are usually annotated with both MutationAssessor and Oncotator; the latter simply enriches the annotation based on the event and it can handle in-del events as well. If you are looking for simple annotation, then I guess Oncotator will do the job for you, but if you would like measure the effect of an in-del variant, then MutationAssessor won't help you there.

As a side note, I saw that you have a v1 prefix in the MutationAssessor URL; I suggest you get rid of it and use the latest version instead, which is v2.