Question: TCGA metastatic samples
1
gravatar for Vasei
4 months ago by
Vasei20
Vasei20 wrote:

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).

tcga • 537 views
ADD COMMENTlink modified 4 months ago by Kevin Blighe33k • written 4 months ago by Vasei20
4
gravatar for Kevin Blighe
4 months ago by
Kevin Blighe33k
Republic of Ireland
Kevin Blighe33k wrote:

I am fairly sure that I have seen samples with code 06 - in fact, almost certain. The number of these samples will differ across cancer and data-type, though. I don't know how samples were selected for profiling - there does not appear to have been any formal agreement among the various centers partaking in the project in this regard.

Note that patients who had a metastatic site are definitively part of TCGA. One can infer this from the clinical data that is held on the GDC Legacy: BRCA

Sample:

barcode         new_tumor_event new_neoplasm_event_type new_neoplasm_event_occurrence_anatomic_site
TCGA-A2-A0T7    NO              [Not Available]         [Not Available]
TCGA-A2-A0YC    YES             Locoregional Disease    [Not Available]
TCGA-A2-A0YC    YES             Distant Metastasis      Bone
TCGA-A2-A0YG    NO              [Not Available]         [Not Available]
TCGA-A2-A0YH    NO              [Not Available]         [Not Available]
TCGA-A2-A0YI    NO              [Not Available]         [Not Available]
TCGA-A2-A0YJ    YES             Distant Metastasis      Other, specify

To select out these files, search for your cancer of interest (via the checkboxes at left on the GDC Legacy), and select the Clinical data and Biotab format.

ADD COMMENTlink written 4 months ago by Kevin Blighe33k
1
gravatar for Kevin Blighe
4 months ago by
Kevin Blighe33k
Republic of Ireland
Kevin Blighe33k wrote:

A second answer to programmatically obtain all metastatic TCGA samples, or those for a particular study:

library(GenomicDataCommons)

1, Metastatic TCGA-BRCA

response <- cases() %>%
  filter(~ project.project_id=='TCGA-BRCA' & samples.sample_type=='Metastatic') %>%
  GenomicDataCommons::select(c(default_fields(cases()), 'samples.sample_type')) %>%
  response_all()

nrow(response$results)
[1] 7

2, All TCGA metastatic samples

response <- cases() %>%
  filter(~ project.program.name=='TCGA' & samples.sample_type=='Metastatic') %>%
  GenomicDataCommons::select(c(default_fields(cases()), 'samples.sample_type')) %>%
  response_all()

nrow(response$results)
[1] 398

table(response$results$primary_site)
 Adrenal Gland       Bladder        Breast        Cervix    Colorectal 
            2             1             7             2             2 
    Esophagus Head and Neck      Pancreas      Prostate          Skin 
            1             2             1             1           370 
  Soft Tissue       Thyroid 
            1             8
ADD COMMENTlink modified 4 months ago • written 4 months ago by Kevin Blighe33k
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