I hope my message reaches everyone healthy and safe !! I was not sure if I should post my question/issue here, but probably due to the discrepancy of my initial stratification results, I decided to post it here:
briefly, just before some weeks ago, based on a current project, I utilized the cell line selector, to download the available colorectal cancer cell lines, along with the respective mutational status I can add amongst the search (file attached) as also how I added the mutation information (attached plot)
My ultimate rationale, is to stratify the cell lines based on the mutational status of specific genes like: KRAS mutated, BRAF mutated and RAS_RAF_WT (without any additional NRAS/HRAS/RAF1 muts); as our ultimate goal is to identify any specific dependencies in each subgroup, to compare and utilize with our “in-house” patient data;
On this premise, while then I was checking directly the DepMap portal, querying specific cell lines, I found various important discrepancies:
For example in cell line CL11: CL11 DepMap Cell Line Summary in the portal, when querying the mutations tab, for KRAS it returns only “other-non conserving” mutations, whereas from Cell line selector, KRAS has a hotspot value;
This is unfortunately evident for other cell lines, with noticeable differences;
Thus, my critical questions are the following:
Should indeed be differences between the cell line selector and the actual DepMap portal? Or my rationale is incorrect and I should downloaded differently the cancer cell lines of interest along the mutational data?
If my notion is correct, I should only then use the DepMap portal and query each colorectal cell line separately? to check the mutational status in order to stratify accordingly? And the only information to keep from the CellLine selector is just the column lineage2 if the respective cell line is colorectal by the column ?
Finally, one other very crucial question regarding the interpretation of mutations: as in my project we are focusing on protein coding mutations, which types of mutations should I keep as most “important”? Only hotspot and damaging?
In addition, the label “Other” does not mean a presence of mutation for this particular gene, correct? And other-non conserving has a different translation?
Thank you in advance