COSMIC hotspot mutations

Q&A
1

Hi everyone, I want someone to explain to me:

  1. The difference between the “damaging_effect.csv” and “hotspot.csv” files?
  2. What does it mean the column “CosmicHotspot” in the “OmicsSomaticMutations.csv” file?

Best,
Amare

2

Hi Amare,

  1. Can you clarify what files you are referring to? Do you mean OmicsSomaticMutationsMatrixDamaging.csv and OmicsSomaticMutationsMatrixHotspot.csv in the current release?
  2. CosmicHotspot is a boolean column that indicates if a variant has more than 5 overlapping mutations from COSMIC in different tissues. I’d like to note that we realized that this column was based on outdated annotation sources, and it will be retired in the upcoming 23Q4 release. The new release will not have a COSMIC column explicitly, but we do use updated COSMIC variant tier information to inform our filtering process. Please stay tuned and refer to our latest documentation in 23Q4.

Thanks,
Simone

3

@simz, Thank you for addressing my question. In the custom downloads (DepMap Data Downloads), there are files and I was referring to the hotspot mutation and damaging mutation files. However, do they differ from the file you stated above (OmicsSomaticMutationsMatrixDamaging.csv and OmicsSomaticMutationsMatrixHotspot.csv)?
Best,
Amare

4

Hi Amare,

The ones in the custom download page are the same as OmicsSomaticMutationsMatrixDamaging and OmicsSomaticMutationsMatrixHotspot.

Please refer to our 22Q4 documentation for specific definitions of damaging and hotspot mutations. Similar to the main mutation file, the definitions for these two matrices are also going to change in the 23Q4 release as part of our pipeline update. Updated documentation will be linked in the download page then.

Thanks,
Simone

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