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docs: document DepMap mutation scores #53

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13 changes: 13 additions & 0 deletions datasets/depmap/README.md
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Expand Up @@ -45,6 +45,19 @@ Started processing with the FADU cell line:
## Config
Example Config file used to get preliminary results on OmicsIntegrator1 and 2 following the EGFR dataset example. Will test out more parameters and update.

## Data types
The variant (i.e. mutation) scores from DepMap are originally described as
> A variant is considered a damaging mutation if LikelyLoF == True. (0 == no mutation; If there is one or more damaging mutations in the same gene for the same cell line, the allele frequencies are summed, and if the sum is greater than 0.95, a value of 2 is assigned and if not, a value of 1 is assigned.)

Our interpretation of this is
- 0: their variant scoring algorithm assesses this variant to be not functional, that is, not damaging, so we ignore it when assigning prizes
- 1: their scoring algorithm assesses the variant to be functional and it occurs less than all the time (AF < 0.95), which can happen in many ways in cancer (there are multiple clones in the tumor, there is a single clone but one copy of the gene has the mutation and one doesn't); there could also be multiple different mutations in the same gene but they all have frequencies that still sum to less than 0.95
- 2: the gene is predicted to be severely functionally impacted because there are multiple different mutations each assessed to be functional, and cumulatively they have allele frequency approaching 1 or more

We retain the difference in score of 1 or 2 because genes with a score of 2 are more important than genes with a score of 1, per the DepMap scoring scheme.
The DepMap [pipeline documentation](https://storage.googleapis.com/shared-portal-files/Tools/25Q3_Mutation_Pipeline_Documentation.pdf) provides more information about how they derive the original scores, such as VEP for variant effect prediction and gnomAD for allele frequencies.


## Release Citation
For DepMap Release data, including CRISPR Screens, PRISM Drug Screens, Copy Number, Mutation, Expression, and Fusions:
DepMap, Broad (2025). DepMap Public 25Q2. Dataset. depmap.org
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