Definition of Solid Tissue Normal

[Leung,Sze L]

Hi,

 

I am analyzing PDAC samples data from TCGA, would you please let me know what does it mean for "NT: Solid Tissue Normal" (http://gdac.broadinstitute.org/runs/stddata__latest/samples_report/PAAD.html). Are those normal samples from the pancreas of normal people or normal tissue adjacent of PDAC tumors?

 

Thank you very much!

 

Best,

Cecilia

Postdoctoral Fellow

UT MD Anderson Cancer Center

 

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[Michael Noble]

Dear Cecilia,

It is the latter: they are adjacent normal tissue from the same patient that the tumor sample was collected.  If you’d like more detailed information, please see these links

https://confluence.broadinstitute.org/display/GDAC/FAQ#FAQ-sampleTypesQWhatTCGAsampletypesareFirehosepipelinesexecutedupon

https://confluence.broadinstitute.org/display/GDAC/FAQ#FAQ-sampleTypesDiscoveryQHowdoIanalyzesamplesthatarentincludedinyourFirehoserunsegBloodNormalsSolidTissueNormalsetc

in our online FAQ, and follow the links therein back to TCGA sources.  

Lastly, if you’d like a set of normal tissue from essentially disease-free donors for use in your research, see the GTEX consortium.

Best,

Mike

—

Michael S. Noble

Associate Director for Data Science

Cancer Genome Computational Analysis

The Broad Institute of MIT & Harvard

Manager, Genome Data Analysis Center

The Cancer Genome Atlas

[caotran...@gmail.com]

Hi,

I am analyzing Liver cancer transcription profiling data on GDC - Data portal from TCGA, and I would like to sort out HBV and HCV type of infection of those liver cancer patients. Could you please give me any solution to this problem?

Thank you very much!

Ngoc

Vào 23:34:03 UTC+7 Thứ Năm, ngày 14 tháng 7 năm 2016, Leung,Sze L đã viết:

[Michael Noble]

Hello,

Our understanding is that questions about data obtained from the GDC portal can be submitted to the GDC, as described here.

Best,

Mike

---

Michael S. Noble

Associate Director for Data Science

Cancer Genome Computational Analysis

Broad Institute of MIT and Harvard

[caotran...@gmail.com]

Hi,

Thank you for your response. But my question really is how to achieve clinical data about HBV and HCV in liver cancer patients from GDC.

Thank you!

Ngoc

 

Sent from my Windows 10 phone

[Michael S. Noble]

I still don't understand: Aren't the GDC staff the best possible source of help for using GDC data?