Forum

I got the HER2, ER, PR status of BRCA patients from the BRCA TCGA publication supplementary:

https://www.nature.com/articles/nature11412#supplementary-information

filename: TCGA_Supplementary Tables 1-4.csv
column: HER2_Final_Status

But since it is from 2012, after some months, I downloaded the newer clinical data from cbioportal**:

http://www.cbioportal.org/study?id=brca_tcga#clinical

filename: data_bcr_clinical_data_patient.txt
columns: IHC-Status, HER2 fish status

However, I noticed that hundreds patients had different her2 status then they had in the old tcga publication:

Barcode IHC-status(cbioportal) Her2 fish status (cbioportal) HER2_Final_Status(tcga publication)
TCGA-A1-A0SH Equivocal Negative Negative
TCGA-A2-A04U Negative Positive Negative
TCGA-A2-A0T2 Negative Not Evaluated Negative
TCGA-A8-A06R Positive Positive Equivocal

At first, I thought there is a method to convert both ihc and fish statuses into one (final status). But I failed to find such method.
In TCGA-A1-A0SH, it seems Fish is prefered.
In TCGA-A2-A04U , it seems it is IHC.
in TCGA-A8-A06R it is neither.

**I verified that for those 4 patients, her2 status is consistent between cbioportal and current TCGA clinical files. (her2_fish_status, her2_status_by_ihc in clinical files)

Thanks in advance,
Maor