Is Microsatellite instability data available for DEPMAP cell lines?

Q&A
1

Is MSI status available for the cell lines in DEPMAP or is there a specific way that this can be calculated using the data currently available?

2

Hi,

We are currently beta testing MSI scores generated by MSIsensor2 as a new feature. We are hoping to release it publicly in the near future. Stay tuned!

Best,
Simone

3

Hi there!
May I follow up on this? The beta features contains a file called OmicsSignatures.csv with the output of MSIsensor2 (MSIscores) which is great. In addition there is a nice publication ( The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity | Nature) that shares their data (Suppl 7) on MSI annotation. They use the tool Indelocator and a collection of cutoffs and thresholds. These two sources are -to the best of my knowledge- the best MSI annotation I know of…am I missing something here? Is there a consensus which one to use (maybe one is more comprehensive than the other?

Thx and Best,
Fio

4

Hi @fschischlik ,

Thanks for bringing it to our attention! We have not tested Indelocator on our samples, so I can’t speak on which tool performs better/is more comprehensive. We don’t have any concrete plans to add other MSI tools in the immediate future, but it would definitely be interesting to test out Indelocator and see how it compares. We will keep our users updated!

Thanks,
Simone

5

Thank you. This is great!