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Finding Mutation status of IDH1 from FireBrowse data

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 :)

firebrowse mutation rnaseq
• 4,106 views • link
written by lawarde.ankita1 • lawarde.ankita1

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.

• 1 views • link
written by Kevin Blighe Kevin Blighe

Thank you for your suggestions. I really appreciate it.

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written by lawarde.ankita1 • lawarde.ankita1

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

• 0 views • link
written by Researcher Researcher

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

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written by Kevin Blighe Kevin Blighe

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.
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updated by Kevin Blighe Kevin Blighe • written by Researcher Researcher

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

Any help would be appreciated. Thanks.

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written by Researcher Researcher

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?

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written by Kevin Blighe Kevin Blighe

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

• 0 views • link
written by Researcher Researcher

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.

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written by Kevin Blighe Kevin Blighe

Yes I used TCGAbiolinks and it worked for me. Thanks

• 0 views • link
written by Researcher Researcher

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