Finding Mutation status of IDH1 from FireBrowse data

Question

[lawarde.ankita1]

Hello everyone,

I'm using GBM data from FireBrowse. I have RNAseq data downloaded from FireBrowse ( file name: GBM.rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes_normalized__data.data) it has total 171 samples.

I want to find the IDH1 mutations in the samples of GBM data. By following this video () i was able to find the samples with IDH1 mutation. Following is the list of those samples: total 14 samples

TCGA-06-0128-01A-01D-1490-08

TCGA-06-2570-01A-01D-1495-08

TCGA-06-6389-01A-11D-1696-08

TCGA-06-6701-01A-11D-1845-08

TCGA-15-1444-01A-02D-1696-08

TCGA-26-1442-01A-01D-1696-08

TCGA-32-4208-01A-01D-1353-08

TCGA-02-2483-01A-01D-1494-08

TCGA-06-0129-01A-01D-1490-08

TCGA-06-5417-01A-01D-1486-08

TCGA-14-1456-01B-01D-1494-08

TCGA-14-4157-01A-01D-1353-08

TCGA-19-2629-01A-01D-1495-08

TCGA-27-2521-01A-01D-1494-08

so according to the sample barcode, thses are the DNA samples. thus to find the RNA samples form the expression set data i matched samples barcode by substituting "D" by "R" for example : TCGA-27-2521-01A-01D-1494-08 -> TCGA-27-2521-01A-01R-1494-08 and i got only 8 samples in the RNAseq data. But i'm not sure if this is correct way to find samples with mutation in the RNAseq data (expression set). (please give suggestion for this process)

My questions:

1) How to identify the mutation status of samples ?, mutation of interest: IDH1

2) how to find wild type samples for those identified samples.

Thank you all in advance :)

[Kevin Blighe]

I'm neither sure that that's the best approach. Just match them by the shortened TCGA barcode, i.e., TCGA-27-2521. Otherwise, you may find minimal matching.

The wild-type 'normal' mutation data is controlled/restricted access only. You will find 'normal' RNA-seq expression data, though.

[lawarde.ankita1]

Thank you for your suggestions. I really appreciate it.

[Researcher]

Hi,

I tried to follow your instructions to get the Url for LGG samples having IDH1 mutation. But the URL didn't work when I copied this to my console with wget. Am I doing this correct or there is some other way of downloading this?

Looking forward to your reply. Thanks

[Kevin Blighe]

Hey, can you show the exact commands that you used and provide a reproducible example?

[Researcher]

Sure, here it is with the error it got.

[bm@cn4262 LGG]$ wget http://firebrowse.org/api/v1/Analyses/Mutation/MAF?format=tsv&cohort=LGG&tool=MutSig2CV&gene=IDH1&page=1&page_size=250&sort_by=cohort


[1] 37587
[2] 37588
[3] 37589
[4] 37590
[5] 37591
[6] 37592
[2]   Done                    cohort=LGG
[3]   Done                    tool=MutSig2CV
[5]-  Done                    page=1
[bm@cn4262 LGG]$ --2019-02-13 17:13:01--  http://firebrowse.org/api/v1/Analyses/Mutation/MAF?format=tsv
Resolving dtn02-e0 (dtn02-e0)... 10.1.200.238
Connecting to dtn02-e0 (dtn02-e0)|10.1.200.238|:3128... connected.
Proxy request sent, awaiting response... 400 Bad Request
2019-02-13 17:13:01 ERROR 400: Bad Request.

[Researcher]

Can you please help.....? I really got stuck.

Any help would be appreciated. Thanks.

[Kevin Blighe]

You received HTTP error code 400, which means that the server could not parse the URL that you provided.

What, exactly, are you trying to do? Where did you even find that URL?

[Researcher]

I want to find all those LGG samples who have IDH gene mutation. Isn't it the correct way to do this? Can you please suggest any alternative method for the same.

Thanks

[Kevin Blighe]

I do not know if it is the right way. From where did you get the information to run this command:

wget http://firebrowse.org/api/v1/Analyses/Mutation/MAF?format=tsv&cohort=LGG&tool=MutSig2CV&gene=IDH1&page=1&page_size=250&sort_by=cohort

Did you see this is some tutorial?

Please check the clinical and somatic variant data for LGG at the GDC Data Portal. I have configured a search for you, HERE

[Researcher]

I found this very helpful.

http://bioinformaticsfmrp.github.io/TCGAbiolinks/subtypes.html

Thanks

[Kevin Blighe]

If you wish to use TCGAbiolinks to obtain your mutation data, then I can tell you that it is a very common R package for obtaining TCGA data.

[Researcher]

Yes I used TCGAbiolinks and it worked for me. Thanks