1p19q co deletion in the TCGA LGG dataset

[Huebner, Alexander]

Hi,

 

I was wondering if you could help me out with something.

I am trying to identify the samples within the TCGA LGG dataset that have 1p19q codeletion.

According to your summary of that dataset there are 85 IDH1mut/1p19q codeleted samples.

However when looking at the CNV data I can’t seem to find any information on that.

If you could point me in the right direction I would highly appreciate that.

 

Best regards

 

Alexander Huebner

 

 

Alexander Huebner

 

Visiting Scholar

The Ohio State University Comprehensive Cancer Center

Arthur G. James Cancer Hospital and Richard J. Solove Research Institute

Radiation Oncology Department

410 W. 12th Ave

351 Wiseman Hall

Columbus, Ohio 43210

( (614)685-4242 * Alexande...@osumc.edu

 

 

 

[Huebner, Alexander]

[Nikolaus Schultz]

Hi Alexander,

These deletions are usually only heterozygous (single copy). You could use the OncoQuery Language (OQL) to identify samples with het loss of representative genes in these regions. You can find details about how to use OQL here:

http://www.cbioportal.org/public-portal/onco_query_lang_desc.jsp

Unfortunately, there is no way to define arm-level events in cBiopPortal.

Niki.

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