Question: TCGA 2011 Ovarian Data Germline BRCA1/2 status
1
gravatar for Les Ander
3.5 years ago by
Les Ander110
United States
Les Ander110 wrote:

Hi

Does anyone know how I can obtain the germ line status of BRCA1/2 mutations in the TCGA OV 2011 Nature paper?

The supplementary site is here https://tcga-data.nci.nih.gov/docs/publications/ov_2011/ but there is no information on the germline mutations.

In general, how can one obtain the germline mutation data for publicly available published TCGA data? Is this information available for access level 3?

 

tcga • 1.3k views
ADD COMMENTlink modified 3.0 years ago by michael.d.mclellan140 • written 3.5 years ago by Les Ander110
1
gravatar for Cyriac Kandoth
3.5 years ago by
Cyriac Kandoth5.2k
Memorial Sloan Kettering, New York, USA
Cyriac Kandoth5.2k wrote:

TCGA had stricter policies back then when the TCGA OV marker paper was published. If there was a precedent to look at the germline status of any genes, then it was performed as a supplementary analysis, and uploaded in the protected DCC area, or the TCGA Jamboree. Currently, I think TCGA BRCA and UCEC are the only marker papers where germline mutation status was publicly reported for a few handpicked genes.

For TCGA OV, your best bet is to use the data from this publication - http://www.ncbi.nlm.nih.gov/pubmed/24448499 - Supplementary data files 4, 11, 12, and 13 should have more than what you need.

ADD COMMENTlink written 3.5 years ago by Cyriac Kandoth5.2k

Thank you so much for the helpful reply Cyriac. I checked Supplementary Table 4, despite the fact the title suggests that the table has germline mutations, all the BRCA1/2 mutations are labeled as "somatic" and also the sample identifiers are not given. Table 11,12 and 13 has some BRCA1 and 2 mutations (and judging from the title of the table they are suppose to be germline) but again no TCGA sample id is given.

Do you know where I can get the list of TCGA sample names that have germline BRCA1 and 2 mutations?

Thank you

 

ADD REPLYlink written 3.5 years ago by Les Ander110

Wow ok... that's not nice. If they just wanted to further de-identify the patients, they could have used different sample barcode rather than exclude them outright. You can try contacting the corresponding author - http://www.nature.com/ncomms/foxtrot/svc/authoremailform?doi=10.1038/ncomms4156&author=Li+Ding

ADD REPLYlink written 3.5 years ago by Cyriac Kandoth5.2k
1
gravatar for michael.d.mclellan
3.0 years ago by
United States
michael.d.mclellan140 wrote:

The BRCA1/2 germline variants reported in the 2011 publication were removed from the webpage on the NIH site at https://tcga-data.nci.nih.gov/docs/publications/ov_2011/ because policy revisions relabeled even single germline variants as protected data.

They were originally published in Supplementary Table 8. http://www.nature.com/nature/journal/v474/n7353/extref/nature10166-s1.pdf

TCGA germline variants with sample information are protected data - to obtain them requires applying for access as described here:

http://cancergenome.nih.gov/PublishedContent/Files/pdfs/TCGA%20Human%20Subjects%20Protection%20and%20Data%20Access%20Policies%20Rev_2014-01-16.pdf

ADD COMMENTlink written 3.0 years ago by michael.d.mclellan140
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