I was wondering if anyone could point me to the experimental methods used to generate the data that is used to calculate the probability of dependency.
The methodology for computing the probability of dependency is described in
Dempster, J. M., Rossen, J., Kazachkova, M., Pan, J., Kugener, G., Root, D. E., & Tsherniak, A. (2019). Extracting Biological Insights from the Project Achilles Genome-Scale CRISPR Screens in Cancer Cell Lines. BioRxiv , 720243.
Thank you for the paper, I had previously found it and only quickly skimmed over it. Having read it in a bit more detail, am I correct in that dependency is calculated purely from computer analysis? As a more benchtop scientist, I’d assumed cell line dependency would be calculated by CRISPR knockout of a gene using multiple sgRNAs, followed by comparing growth of these knockouts to the normal cell line.
The reason for my enquiry is since CRISPR involves the cell repairing the induced dsDNA breaks, if you knocked out a gene involved in dsDNA repair, it seems logical for this to potentially impact the dependency score. I was thus wondering whether this was an issue that was accounted for?