Mutation importance calculator

Q&A
1

Dear DepMap community,

Greetings, thank you for your sharing the public datasets for genetic information.
I have a simple question about the mutation information.
I’m wondering that are there any methods for calculating the importance of mutations per gene using the mutation.csv file in the DepMap portal.
(E.g., the mutations in BRAF are more important in A cancer type than other genes)

I confirmed MutSig and CHASMplus for the mutation importance calculator, but I thought the input files for them are not relevant to DepMap mutation.csv file.
Can anyone recommend the proper methods?

Sincerely,
Songyeon

2

Hi SonSong,

I don’t really know how we can help you here. Tools like CHASM can help in defining importance as Loss of Function but even then this is not per cancer type.

We haven’t looked into this much but there might be some COSMIC hotspot annotations that are cancer specific that you can use.

I think in your question you need to figure out what you mean by importance.

Hope it helps,
Best,

3

Dear jkobject,

Thank you for your reply.
Also, I’m sorry for asking an unnecessary question to you.

I’m searching for the method that can utilize mutation.csv file in the DepMap portal which is MAF file format.
I expected the result similar to dependency score matrix as below:
|_______| Bone | Breast | … | Thyroid |
| Gene A | 0.034 | 0.298 | … | 0.149 |
| Gene B | 0.304 | 0.192 | … | 0.008 |
where the higher score means the more significantly mutated in the cancer type.

I found CHASM(plus), Mutsig, and Mutagene for this work, but I’m not sure whether these tools are appropriate or not.
Again, sorry for disturbing you, and have a nice day.
Sincerely,