Comprehensive Annotation Of Luminal/Basal For Breast Cancer Cell Line Microarray

Question

[user]

I am analyzing CCLE microarray (http://www.broadinstitute.org/ccle/home) data from the Broad/Novartis project. The dataset contains microarray data for many breast cancer cell lines, including breast cancer cell lines. I can't find an annotation of the breast cancer cell lines anywhere and I am sure it comes up a lot for others. Where can one find an annotation of the basic properties of breast cancer cell lines (e.g. HER2 / PR status, and Luminal vs. Basal when applicable) for these lines?

I could find a subset of the cell lines in this paper (http://www.ncbi.nlm.nih.gov/pubmed/17157791) but by no means all. For example I can't find the Luminal vs. Basal annotation or HER2/PR status for these lines:

        EVSAT                 
       CAL851                 
     Hs 606.T                 
        HMC18                 
     Hs 739.T                 
         YMB1                 
     Hs 281.T                 
     Hs 274.T                 
     Hs 343.T                 
       CAL120                 
        JIMT1                 
       CAL148                 
      HCC1599                 
        HDQP1                 
     Hs 742.T                 
         HMEL

Is there a simple text (tsv/csv) file that gives the annotation for these? thanks.

Answer 1

[Charles Warden]

I don't know if it will work in all cases, but you can find some patient characteristics from the ATCC website. For example, here is the link for HCC1599:

http://www.atcc.org/products/all/CRL-2331.aspx

For example. you can tell that this was from a triple-negative patient. This isn't exactly the same as the molecular subtype, but it is related.

I'm guessing samples like "Hs 343.T" will be harder. They sound like primary cell line IDs. Perhaps you can contact CCLE support for more info?

http://www.broadinstitute.org/ccle/support/esupport/35480/;jsessionid=4D2956305AFAEC19E7C5921B024A13B2