TCGA sample mapping?

[sigven]

Hi,
Thanks for a very comprehensive resource! I have compiled a list of unique diagnoses assigned to TCGA patients/samples. I was wondering whether there exist a mapping somewhere between OncoTree codes and the diagnoses/primary_tissues assigned to TCGA samples? Since OncoTree is used in cBioPortal, I reckoned that this may exist somewhere, but I may be wrong.

regards,
Sigve

[ritikakundra]

@sigven Here is the mapping:
TCGA_ONCOTREE_MAPPINGS.xlsx
Let us know if you have any questions.

[sigven]

Hi @ritikakundra,
Thanks for the response. Considering the > 100 different tumor subtypes/diagnoses within TCGA samples which I pointed to, this mapping was not exactly what I was looking for. The mapping you point to refers to the main tumor types only. Considering the depth and detailed subtypes within OncoTree, I was looking for a more fine-grained mapping. I guess then that this mapping is not something you or others have at hand?

best,
Sigve

[ritikakundra]

All TCGA samples in the portal do have an oncotree assigned to them. I think I can get you that too based on your list.

…

________________________________ From: Sigve Nakken <[email protected]> Sent: Thursday, August 29, 2019 5:11:03 AM To: cBioPortal/oncotree Cc: Kundra, Ritika/Sloan Kettering Institute; Mention Subject: [EXTERNAL] Re: [cBioPortal/oncotree] TCGA sample mapping? (#200) Hi @ritikakundra<https://github.com/ritikakundra>, Thanks for the response. Considering the > 100 different tumor subtypes/diagnoses within TCGA samples which I pointed to, this mapping was not exactly what I was looking for. The mapping you point to refers to the main tumor types only. Considering the depth and detailed subtypes within OncoTree, I was looking for a more fine-grained mapping. I guess then that this mapping is not something you or others have at hand? best, Sigve — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub<#200?email_source=notifications&email_token=AC3TTNVCSQRNEFJ4WZFGVFDQG6HCPA5CNFSM4IMF2FH2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD5N2BPI#issuecomment-526098621>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AC3TTNUP54PYVTHMSJ7ATGTQG6HCPANCNFSM4IMF2FHQ>. ===================================================================== Please note that this e-mail and any files transmitted from Memorial Sloan Kettering Cancer Center may be privileged, confidential, and protected from disclosure under applicable law. If the reader of this message is not the intended recipient, or an employee or agent responsible for delivering this message to the intended recipient, you are hereby notified that any reading, dissemination, distribution, copying, or other use of this communication or any of its attachments is strictly prohibited. If you have received this communication in error, please notify the sender immediately by replying to this message and deleting this message, any attachments, and all copies and backups from your computer.

[yesitsjess]

Hi @ritikakundra,
Thanks for the response. Considering the > 100 different tumor subtypes/diagnoses within TCGA samples which I pointed to, this mapping was not exactly what I was looking for. The mapping you point to refers to the main tumor types only. Considering the depth and detailed subtypes within OncoTree, I was looking for a more fine-grained mapping. I guess then that this mapping is not something you or others have at hand?

best,
Sigve

I'm looking for this mapping file too, was there any solution to this issue in the end?

[jkobject]

Hello Looking for that mapping as well.

Best,

[yesitsjess]

It wasn't quite what I was looking for, but this might be useful: https://bioconductor.org/packages/devel/bioc/vignettes/BiocOncoTK/inst/doc/maptcga.html

[jkobject]

Yes so I guess TCGA does just have 35 tumor types? (compared to the >800 that oncotree lists).