Question: Help finding specific breast cancer datasets
gravatar for ogola89
4 months ago by
ogola890 wrote:

Hi All,

I am pretty new to bioinformatic analysis and so I apologize if this seems like a simple/redundant question. I am wondering whether specific datasets are available - or how to filter existing datasets to find specific data.

I am looking for RNA-Seq data, for breast cancer which has metastasized to the bone, so RNA-seq of the secondary tumour. Furthermore, I would like to access data as to the time to recurrence so I can identify how long it took to outgrowth in the secondary site.

Please help me identify how to go about finding the data for this type of specificity.

Thank you.

bone breast cancer metastasis • 149 views
ADD COMMENTlink modified 4 months ago by Kevin Blighe48k • written 4 months ago by ogola890
gravatar for Kevin Blighe
4 months ago by
Kevin Blighe48k
Kevin Blighe48k wrote:

TCGA has 17 [breast] primary tumour samples that eventually metastasised to bone; however, the RNA-seq is of the primary tumour. In total, only 7 breast cancer samples in TCGA are actual metastatic samples, and none of these are bone mets, from what I can see. I got this information from my 2 answers, here: C: TCGA metastatic samples

Then there is this study that looked at bone mets, but it is microarray data: Latent bone metastasis in breast cancer tied to Src-dependent survival signals (GSE14020)

Probably your best bet is to browse the curated datasets at the relatively new Human Cancer Metastasis Database. Go to Browse, filter for 'breast cancer', and then look for 'bone' in the Metastasis Site column.


ADD COMMENTlink modified 4 months ago • written 4 months ago by Kevin Blighe48k
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