Question: Find Her2 copy number by FISH in TCGA BRCA clinical file
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gravatar for Sebastian Boegel
4.3 years ago by
Germany
Sebastian Boegel460 wrote:

Hi all,

i downloaded the clinical annotation file (Biotab format) for TCGA BRCA from the data matrix in order to look at Her2 copy number measured by FISH (something wich is done in clinical routine). I found the column with the annotation

her2_copy_number

her2_neu_breast_carcinoma_copy_analysis_input_total_number

 

The TCGA BCR Dictionary (https://tcga-data.nci.nih.gov/docs/dictionary/TCGA_BCR_DataDictionary_v2.3.xml) sais to this column: "Result of HER2 Copy Number testing (for the metastatic tumor), expressed as a range of values"

I am now confused because of 2 things:

1.) I do not see range of values, just one value

2.) i see many high values like 185. I cannot belive, that this is the copy number of Her2 (in clinics CN>6 is said to be positive).

Question: am i looking at the right column to find out the CN of Her2 measured by FISH?

 

Thank you for your help

ADD COMMENTlink written 4.3 years ago by Sebastian Boegel460
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