Her2 status in TCGA clinical data

Question

[afzaljf911]

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.

Answer 1

[Kevin Blighe]

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

[afzaljf911]

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

[mrpaul]

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".

[afzaljf911]

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