TCGA CNV data 1p/19q codeletion (whole arm deletion)

Question

[kwanghoon]

Hi, I'm trying to get 1p 19q codeletion data from TCGA-GBM,LGG data.

I got CNV data of GBM, LGG and sorted chr1,19 that segment_mean <= -0.3 using R. (https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/CNV_Pipeline/)

If 1p/19q codeletion is exist, diagnosis can be "Oligodendroglioma". Not just deletion, I should find whole arm deletion at chr 1p and chr 19q codeletion.

What should I do...

[Yingping]

Hi, I encountered the same problem, I spent about one week working on it, but I still can not find a solution.

Could you please share how you finally download the IDH mutation status and 1p/19q codeletion status data of TCGA-GBM and TCGA-LGG datasets? Thanks a lot in advance!

[Kevin Blighe]

Hi, I think that the solution is as follows: if the information is not available in the clinical data, then you will have to define IDH status yourself, and also detect the co-deletion. It seems that IDH status may be available in the work linked by gabriel.rosser (see below)

[Yingping]

Hi Kevin, thanks a lot for your kind reply. I finally find a way to download the IDH mutation status and 1p/19q codeletion status of TCGA-GBM and TCGA-LGG datasets. I put it here for future researchers:

***Using the following R code**

library(TCGAbiolinks)

library(openxlsx)

lgg_subtype <- TCGAquery_subtype(tumor = "lgg")

write.xlsx(lgg_subtype, file = "lgg_subtype.xlsx")

gbm_subtype <- TCGAquery_subtype(tumor = "gbm")

write.xlsx(gbm_subtype, file = "gbm_subtype.xlsx")

See more details here: https://www.bioconductor.org/packages/release/bioc/vignettes/TCGAbiolinks/inst/doc/subtypes.html

[Kevin Blighe]

Excellent work - thanks. So, this information must have been in PanCancerAtlas clinical information. Noted for future!

Answer 1

[Kevin Blighe]

Hi, you implied that you have already obtained the data. So, please proceed with your analysis.

You will have to develop some code that identifies deletion of the entire chromosomal arms. You can create rules that define whether an arm is deleted or not.

By the way: within the LGG (Lower Grade Glioma) TCGA cohort are already-identified oligodendroglioma samples (n=191). Please search the associated clinical data for LGG. The file is the BCR Biotab file, nationwidechildrens.org_clinical_patient_lgg.txt, available at the GDC Data portal.

To clarify: Lower Grade Glioma (LGG) is already classified into

• Astrocytoma
• Oligodendroglioma
• Oligoastrocytoma

I was analysing these samples just a few weeks ago.

Kevin

[kwanghoon]

Hi Kevin. Thank you for your nice reply.

I know there is classified dx, but I was trying to check 1p/19q whole arm codel in Oligodendroglioma which is classified into "NOS" or "Anaplastic".

Do you think I don't need to do this?

Thank you again!

[Kevin Blighe]

it depends what is the ultimate aim of your analysis / project?

[kwanghoon]

I'm trying to check specific gene expression level of brain tumors between GBM, LGG(Astrocytoma, Oligodendroglioma) and including IDH mutataion status.

[Kevin Blighe]

Then I think that you need to proceed as planned. Regarding the chromosomal arm deletions, you can develop some rule for 'aggregating' the copy number from multiple CN segments using the data that you have already obtained. One thing, for example, is to 'bin' each 50 segments and check the frequency of those below -0.3, and then 'slide' this bin across each chromosome, moving by 5 segments each time. There are different ways to do it.

Answer 2

[gabriel.rosser]

This analysis has been carried out previously by Ceccarreli et al.. Look at Table S1 in that publication (column W).

[Elbert]

Thank you. I have found the excel document under your guidance. Your comment really helps me a lot.