Question: Her2 status in TCGA clinical data
0
gravatar for afzaljf911
15 months ago by
afzaljf91120
afzaljf91120 wrote:

Dear all

I am working with TCGA clinical data file for some analyses. I need Her2 status in breast cancer patients. There are some variables that identify her2 status as positive or negative according IHC and ISH methods. I need to clarify these situations according all existing data.I want to know what are these Variables?

"patient.her2_neu_breast_carcinoma_copy_analysis_input_total_number" "patient.her2_neu_and_centromere_17_copy_number_metastatic_breast_carcinoma_analysis_input_total_number_count" and "patient.her2_neu_and_centromere_17_copy_number_analysis_input_total_number_count"

and also I want to know "patient.lab_procedure_her2_neu_in_situ_hybrid_outcome_type" variable has been identified based an which variable? just patient.her2_neu_chromosone_17_signal_ratio_value? or with another such as copy number of her2? I would be grateful if you could kindly help me.

ADD COMMENTlink modified 15 months ago • written 15 months ago by afzaljf91120
1
gravatar for Kevin Blighe
15 months ago by
Kevin Blighe42k
Kevin Blighe42k wrote:

You will get a definitive answer for HER2 status by obtaining the clinical data in biotab format from the GDC Legacy Archive. The information will be in columns:

  • her2_status_by_ihc
  • her2_ihc_percent_positiv
  • her2_ihc_score
  • her2_positivity_scale_other
  • her2_positivity_method_text
  • her2_fish_status
  • her2_copy_number

Here is a link to the file to which I am referring: https://portal.gdc.cancer.gov/legacy-archive/files/735bc5ff-8...

You will be able to use the patient UUID or TCGA barcode for the purposes of linking this back to your data.

Kevin

ADD COMMENTlink modified 15 months ago • written 15 months ago by Kevin Blighe42k
1

Dear Kevin, Thank you very much for your advice. Your comment was very helpful. Regards, Fahimeh

ADD REPLYlink modified 15 months ago • written 15 months ago by afzaljf91120

So I have that clinical data, but what series or AND/OR gates do I need to determine what is standardly HER2+? For example, I see some entries with her2_status_by_ihc = "Negative", and her2_copy_number = "60".

ADD REPLYlink written 8 months ago by mrpaul0
1

Hi, you can use new ASCO guideline for recategorization: Recommendations for Human Epidermal Growth Factor Receptor 2 Testing in Breast Cancer American Society of Clinical Oncology/College of American Pathologists Clinical Practice Guideline Update

ADD REPLYlink written 8 months ago by afzaljf91120
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