how do I know the breast cancer subtype based on TCGA clinical data

Question

[bxia]

how do I know the breast cancer subtype based on TCGA clinical data?

And the clinical data right now become json format?

Answer 1

[EagleEye]

If you want to analyse independent of any classification you can use integrative clustering method based on expression and other dataset like CNV, methylation etc,, example like in the following articles

1. The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups

   http://www.nature.com/nature/journal/v486/n7403/full/nature10983.html

2. ​BCL11A is a triple-negative breast cancer gene with critical functions in stem and progenitor cells

   http://www.nature.com/ncomms/2015/150109/ncomms6987/full/ncomms6987.html

Answer 2

[EagleEye]

I replied it here in your previous post

C: GENECODE V24 vs V22 vs V19

Writing again,

If you are specifically asking for BRCA tumors with PAM50 classification, refer the BRCA TCGA publication supplementary

Comprehensive molecular portraits of human breast tumours

BRCA Article:

http://www.nature.com/nature/journal/v490/n7418/full/nature11412.html#supplementary-information

Supplementary info:

http://www.nature.com/nature/journal/v490/n7418/extref/nature11412-s2.zip (SuppTable1, contains TCGA patients with PAM50 classification)

[bxia]

So it is researcher defined gene signature subtype, not based on clinical diagnosis assay, right?

[EagleEye]

1) The information from clinical diagnosis are available from TCGA for individual patients (ex, ER+,ER-,PR+,PR.,stages etc.,)

2) These patients from TCGA also classified in the above mentioned study based on PAM50 gene expression based on previous classification (Parker et al., 2009 classified based on 50-gene expression signatures)

More discussions Where To Download Pam50 Gene Set?

[bxia]

Thank you very much,

I just saw your previous post, let me confirm, so TCGA has subtype information, but since the website is down for maintenance, I can't see that in their alternative website GDC...

In the clinical data, there is classification such as ER positive, ER negative, triple negative and so on, right?

Answer 3

[xushutan]

Here is a link for breast cancer survial curve based on TCGA and METABRIC data http://tumorsurvival.org/ Also subtypes are annotated

[EagleEye]

Hi,

Instead of searching and posting individually in all previous posts (older). It will easy for you to just create a new thread (post) with your BRCA survival analysis tool.