MSI annotations

Q&A
1

The sample_info.csv Download shows 18 cell-lines annotated as MSI in the lineage_molecular_subtype field. However, the data explorer provides an option to color cell lines by Microsatellite Instability, and provides two sources for these data: CCLE (NGS) and GDSC (PCR) - both of which include ~60 cell lines. Why the discrepancy? Will the lineage_molecular_subtype field eventually show 60 cell-lines with an MSI annotation?

Thanks

2

Thanks for bringing this into our attention. The sample_info file has not been updated for the new datasets. We will provide this information as a downloadable file in the near future, but for now please rely on the data from the data explorer.

3

Hi,

Thanks for all your work on this project! I was wondering if updated MSI annotations are present in the " DepMap Public 22Q4 Primary Files"? The “Model.csv” file only has 18 cell lines classified as “MSI”.

Thanks for your help!

Best,

Otto.

4

It has been two years since the original question, and the model.csv file has not been updated. Is there another file you can download with the complete annotation of cell lines?

5

MSIscore is now a feature in OmicsSignatures.csv that gets updated for new cell lines every release. MSIscore > 20 is considered MSI, otherwise MSS. Since it is inferred from omics data, we do not include it in model.csv as part of model metadata.

Hope this helps,
Simone