I downloaded clinical data of BLCA and BRCA cancers from firebrowse which provides an easy way to access TCGA project's data. Using sample barcodes with sample type code "06"(according to this link), I could not find any metastatic samples. I also tried to use GDC Data Portal to find metastatic samples but I failed there too! Is there any metastatic sample in TCGA project? If yes which cancer types contain more metastatic samples? Should I use the sample barcode to find metastatic samples?
Note: I think this links states the opposite of what I observed! TCGA Tissue Sample Requirements: High Quality Requirements Yield High Quality Data It states that:
Sample from primary tumor was necessary: A primary tumor is the tumor at the initial site of cancer, not where the cancer may have spread or metastasized, called the secondary tumor. TCGA only studied secondary tumors if they matched to a primary as part of a series (germline, primary and metastasis), or in tumor types for which the primary tumor is rarely diagnosed (such as in melanoma).
Hi
what is the host organ for metastatic cancer in TCGA?
can I get the RNAseq of adjacent normal tissue for metastatic cancer?
Thank you
What do you mean? Do you mean, what are the distant metastatic sites? For example, in breast cancer, a metastatic site may be the brain tissue.
There is matched normal RNA-seq for some of the TCGA cancers.
Actually I have seen the same situation, too. It is not exactly non but most of the cancer data that I also downloaded from firebrowse contains only a few or non-metastatic (code 06) samples.