Difference between the data by "Cancer type" and "Cancer type detailed"

[Sinu Paul]

Hi,

When I do a query by gene, what is the difference between the data by "Cancer type" and "Cancer type detailed" in the "Cancer types summary" tab of the results page? I assume the "detailed" is some kind of break-down of the other, but some entries do not match as I expect. For example, when I query "CDH1" against the "Curated set of non-redundant studies", there are only Bladder Urothelial Carcinoma & Bladder/Urinary Tract in "detailed" but there are Bladder Cancer, Bladder Urothelial Carcinoma & Bladder/Urinary Tract Cancer, NOS in the other (details in the attached file CHD1.xlsx). The data based on "cancer type" shows 23 "absolute counts" for "Bladder Urothelial Carcinoma" but based on the "detailed", there are 47. Could you please give me some insight on this? Also, could you please let me know how the classification is done and is there a way to map each one from the "detailed" to the other one, e.g. any IDs with parent-child relationships?

Thanks,

- Sinu

[Tali Mazor]

Hi Sinu,

As far as I know, Cancer Type and Cancer Type Detailed are populated using the OncoTree ontology: http://oncotree.mskcc.org/#/home & https://ascopubs.org/doi/abs/10.1200/CCI.20.00108   Cancer Type Detailed will reflect one of the nodes on the tree, while Cancer Type will be the 'Main type' associated with each node, visible by hovering over a node in the tree.

However, it does appear that this is not perfectly consistent across all studies, which is what's leading to the inconsistency you've identified. In short, it appears that for samples with Cancer Type Detailed = Bladder Urothelial Cancer, one study is using 'Bladder Urothelial Cancer' as the Cancer Type while all other studies are using 'Bladder Cancer'.

I've created an issue on GitHub to address this: https://github.com/cBioPortal/datahub/issues/1405

I've also cc'ed our lead curator, in case there's something I'm not aware of in how those fields get populated.

-Tali

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[Sinu Paul]

Hi Tali,

Thanks for the quick response and the explanation. 

Best,

- Sinu

---

From: Tali Mazor <tma...@ds.dfci.harvard.edu>
Sent: Thursday, April 22, 2021 2:52 PM
To: Sinu Paul <sinu...@ranchobiosciences.com>; ritika...@gmail.com <ritika...@gmail.com>
Cc: cbiop...@googlegroups.com <cbiop...@googlegroups.com>
Subject: Re: [cbioportal] Difference between the data by "Cancer type" and "Cancer type detailed"

 

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