Cbioportal, 'TCGA, Firehose Legacy' data set

[Yasemin Çakır]

Dear Sir/Madame

I am working a molecular pathologist and I am conducting some invesitigation via CbioPortal. However, I have detected some controversial data. I would be grateful if you help.

I am using SKCM group of ''TCGA, Firehose Legacy'' data set. And I have excluded metastatic cases from my investigation. However, when I have applied necessary filtres, there have been still metastasis heading under the sample type section. Unfortunately, I haven’t understand how these cases are present still although I have excluded metastatic cases.

For more understandable, I am attaching link of my search and some screenshots. Thank you for your time.

Kind regards.

Yasemin Cakir, M.D.

https://bit.ly/3V776mZ

                              

[Benjamin Gross]

Hi Yasemin,

Thank you for your question.  I did a cursory look into your query.  Your question involves three clinical attributes that were collected as part of the TCGA SKCM study.

The following attributes were collected/curated at the “Patient Level”:

American Joint Committee on Cancer Metastasis Stage Code

Neoplasm Disease Lymph Node Stage American Joint Committee on Cancer Code

while Sample Type is collected/curated at the “Sample Level”.  Based on your email, it sound like the samples of type “Metastasis" should be filtered away. Maybe there is a disconnect between the patient level attribute values and the sample level value.  Without knowing the details of the collection effort, its hard to say.  It could be a curation error.  The data was collected by Nation Wide Childrens Biospecimen Core Resource (BCR).  Perhaps they could provide more insight into this matter.

https://www.nationwidechildrens.org/research/areas-of-research/biopathology-center/nci-ccg-project-team/the-cancer-genome-atlas

I hope this helps.

-Benjamin

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[Nikolaus Schultz]

Hi,

Not sure I understand this completely, but it is possible that the primary melanoma was analyzed as part of TCGA, even though metastatic disease was detected elsewhere in the body (resulting in a patient level stage that indicates presence of metastasis at diagnosis). The reverse should be true as well, where a patient is first diagnosed as primary disease only but later develops metastases. 

Or did I misunderstand something?

Niki.

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[Benjamin Gross]

These explanations seem plausible.  Maybe they can be confirmed by looking closer at related attributes, but this type of analysis seems hard to do without having clear definitions & controlled vocabularies at hand.