GENECODE V24 vs V22 vs V19

Question

[bxia]

should I assume that most annotation in this file are exactly same?

which annotation TCGA is using?

[GenoMax]

Not for all. V19 was GRCh37 where as rest are GRCh38. Release history here.

[bxia]

then which annotation TCGA lvl 3 data is using?

[Emily]

Have you tried looking at the documentation?

Answer 1

[EagleEye]

https://browser.cghub.ucsc.edu/search/?study=(phs000178)&state=(live)&limit=15

More information:

https://confluence.broadinstitute.org/display/GDAC/Analysis+Run+Release+Notes

[bxia]

Thank you very much,

Is there anyway to filter the sample by subcancer type? such as triple negative breast cancer?

[EagleEye]

Yes it is possible with some effort,

1) Download the clinical information / histopathological information for all cancer types using the following script (The below compressed file in the link contains script to retrieve the information).

A: Clinical Survival data of TCGA (Since TCGA data download portal is under maintenance, you can try the script once it is back)

2) Download the information about TCGA data or metadata using CgHub

https://browser.cghub.ucsc.edu/search/?study=(phs000178)&state=(live)&limit=15

3) Merge columns 'tcga_barcode' from meta data and 'bcr_aliquot_barcode' from clinical information to integrate available clinical information from appropritate cancer types.

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Or else if you are specifically asking for BRCA tumors with PAM50 classification, refer the BRCA TCGA publication supplementary

Comprehensive molecular portraits of human breast tumours

BRCA Article:

http://www.nature.com/nature/journal/v490/n7418/full/nature11412.html#supplementary-information

Supplementary info:

http://www.nature.com/nature/journal/v490/n7418/extref/nature11412-s2.zip (SuppTable1, contains TCGA patients with PAM50 classification)