I am looking for the data published by Mahmoud Ghandi et. al. doi: 10.1038/s41586-019-1186-3. I noted their datasets are available at the CCLE portal, and the CCLE structural variants (SvABA calls) for 329 cell lines is also listed on Datasets | Cancer Cell Line Encyclopedia (CCLE). But I cant find this file in depmap data portal. Could your please share me more information. Thanks for your help.
I believe the file you’re looking for is CCLE_translocations_SvABA_20181221.xlsx
Is that correct?
Thanks for your kindly help. I am not very sure beacuse I noted that this file contain 328 cell lines but not 329.
Ok, I got that Its beacuse of the authors used HCC1143BL as the normal. So the number of cell lines is correct.
Why there is this discrepancy, I don’t believe I can answer that. You would need to contact the authors of the “Next-generation characterization of the Cancer Cell Line Encyclopedia” paper for answers to that question.
What I can say is that the file and its description were copied from the previous CCLE portal and this one of the files that was published associated with that paper.
Looking at the file, I see it has rows for each variant detected. I wonder if the missing line is a result of one line not having any detectable variants, but that’s really just a guess.