Question: How can I look at nonsense mutations in a particular gene in TCGA data?
1
gravatar for biohack92
4.1 years ago by
biohack92150
United States
biohack92150 wrote:

I have been working with TCGA cancer data to examine expression (RNAseqV2) and methylation (Illumina 450k) data. I want to look at sequencing data, but I'm a bit lost to what sort of information is available through TCGA. I want to examine whether there are nonsense mutations between positions 2000-2500 across all cancer types available in TCGA. What sort of resources/workflow should I expect?

mutations sequence tcga • 1.7k views
ADD COMMENTlink modified 4.1 years ago by Cyriac Kandoth5.2k • written 4.1 years ago by biohack92150
2
gravatar for Nicholas Spies
4.1 years ago by
Nicholas Spies1.0k
United States, St. Louis, The Genome Institute at WUSTL
Nicholas Spies1.0k wrote:

If you are asking whether you can search for non-sense mutations between amino acids 2000-2500 of a particular gene in the TCGA sets, I would suggest using the Mutation Annotation Files (MAFs). These files have already been run through somatic variation calling so you won't have to deal with the sequencing data directly. You can filter out your gene of interest across all the MAF's in perl,awk,grep etc... Then in the amino_acid_change column you can search for integer values between p.2000-p.2500, and trv_type "Non-sense mutation".

 

Hope this helps.

 

Nick

 

ADD COMMENTlink written 4.1 years ago by Nicholas Spies1.0k

Appreciate it! Thank you

ADD REPLYlink written 4.1 years ago by biohack92150
2
gravatar for Cyriac Kandoth
4.1 years ago by
Cyriac Kandoth5.2k
Memorial Sloan Kettering, New York, USA
Cyriac Kandoth5.2k wrote:

For your specific question, your best bet is to query cBioPortal using its Onco Query Language (OQL). For example, the following query gets you all nonsense mutations seen in PTEN across all cancer types:

PTEN: MUT = NONSENSE

We also use the more general term TRUNC that pools together ORF truncating events NONSENSE, NONSTARTFRAMESHIFT, and SPLICE.

If you want to do anything more complicated, then I agree with Nick that you need to get the MAF files. Here's an intro to MAF files: Working with MAF files (Mutation Annotation Format) from the TCGA (The Cancer Genome Atlas)

ADD COMMENTlink modified 4.1 years ago • written 4.1 years ago by Cyriac Kandoth5.2k

Yes, I absolutely agree. cBioPortal is a very powerful resource as well. Thanks for the suggestion and sorry for my oversight!

ADD REPLYlink written 4.1 years ago by Nicholas Spies1.0k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 760 users visited in the last hour