Question: Dataset for Breast Cancer with subtypes based on IHC/FISH
0
gravatar for coolfunkleo
15 months ago by
coolfunkleo0 wrote:

I am looking to download a dataset for breast cancer (microarray or RNA-seq) that has breast cancer classification available from traditional methods such as IHC/FISH to compare with my genetic fingerprint based subtypes. Not looking for those that have PAM50 subtypes. Any recommendations ? Thx

rna-seq • 539 views
ADD COMMENTlink modified 15 months ago by Kevin Blighe45k • written 15 months ago by coolfunkleo0
0
gravatar for Kevin Blighe
15 months ago by
Kevin Blighe45k
Kevin Blighe45k wrote:

TCGA

The TCGA has that information (where available) in the clinical information biotab files. Take a look at my answer here in order to give you an idea for breast cancer: A: How to download triple negative breast cancer RNA-seq fpkm data from GDC.

Edit: Following the first part of the short tutorial in my linked thread, I have just downloaded the breast cancer TCGA data and can already see the following data:

  • er_status_by_ihc
  • er_status_ihc_Percent_Positive
  • er_ihc_score
  • pr_status_by_ihc
  • pr_status_ihc_percent_positive
  • pr_positivity_ihc_intensity_score
  • her2_status_by_ihc
  • her2_ihc_percent_positive
  • her2_ihc_score
  • her2_fish_status

To download other data from the TCGA, you can stay on the GDC Legacy Archive and filter the different checkboxes on the left-hand-side in order to select out whatever you need. A lot of data is open access.

METABRIC

METABRIC also profiled by IHC and FISH, I believe, but it is a more 'locked down' dataset and they (from what I understand personally) are careful about the groups to whom they grant access. Take a look:

Kevin

ADD COMMENTlink modified 15 months ago • written 15 months ago by Kevin Blighe45k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1370 users visited in the last hour