I am interested in one specific subtype of breast cancer cell lines, I was wondering how the cell line subtypes are determined? I couldn’t find the answer to my question in the celligner preprint.
The Celligner subtypes just come from DepMap sample info file from the public 19Q4 data release. The subtypes used in Celligner are a mix of subtypes found in the DepMap sample info columns ‘lineage_molecular_subtype’, ‘lineage_subtype’, and ‘lineage_sub_subtype’. We used a mix of the results of these columns to get degrees of granularity that made sense for each of the lineages. In this case, the breast cancer subtypes come from the ‘lineage_molecular_subtype’ column of the DepMap sample info file, but sorry I’m not sure how that column was determined.
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