Question: TCGA clinical data and code discrepancy
0
gravatar for Devyani
3.3 years ago by
Devyani30
India
Devyani30 wrote:

I was looking into the Thyroid carcinoma data and found that only 8 sample among some 500 odd samples is metastatic from the tumor code i.e it has a code of 06. Rest all are primary tumor. But when I downloaded the clinical information of all samples I find that there are 13 samples where metastatic neoplasm is confirmed. Can I know why this discrepancy? And what should I consider as correct? Thank you
 

clinical data tcga tcga • 1.4k views
ADD COMMENTlink written 3.3 years ago by Devyani30

You didn't say what your sources of information were. Presumably you downloaded two different files so make sure that the samples match between the two files e.g. maybe your second file has metastatic samples that are not in the first one.

ADD REPLYlink written 3.3 years ago by Jean-Karim Heriche18k

These are TCGA thyroid cancer data. There are some 500 samples and from their Bar codes we can know if they are primary tumor or metastatic samples. So from all the samples only 8 have a code of metastatic cancer. But when we look into the clinical data of all the samples there are 5 samples more which are labeled metastatic but their code says it non-metastatic. Hope I am clear now. Thanks

ADD REPLYlink written 3.3 years ago by Devyani30
1

It's possible that the clinical data refers to the patient/case not the sample directly i.e. the patient had a metastatic tumor but the sample available was not diagnosed as metastatic when it was acquired.

ADD REPLYlink written 3.3 years ago by Jean-Karim Heriche18k

Yes that might be true. Can it also mean that the primary tumor tissue was taken and not the metastatic tumor? 

And can you tell me when a metastatic tumor is compared with a non-metastatic one say for any analysis, does it mean the tumor samples from the secondary site (where it has metastasized) is taken and compared to the tumor samples from the primary site (primary tumor) OR is it primary tumor samples which have spread to other sites (i.e have the ability to metastasize) compared to primary tumor samples which have not metastasized. 

Hope I am clear. Thank you.

 

ADD REPLYlink written 3.3 years ago by Devyani30

I have only looked a little into TCGA data and didn't see this information. I suggest you contact their helpdesk for clarification.

ADD REPLYlink written 3.3 years ago by Jean-Karim Heriche18k
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