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-   -   How to search for a known mutation in WGS of disease? (http://seqanswers.com/forums/showthread.php?t=46387)

Noa 09-04-2014 05:23 AM

How to search for a known mutation in WGS of disease?
 
I am working with researchers who have identified a gene mutation which significantly affects protein function.
They want to search all existing NGS (esp cancer) data to see whether this protein occurs in diseased tissue (and not just in the cell line they are studying).

Just to clarify- basically what we need to do is essentially look for a particular region of a particular gene to search for a mutation by going through as much WGS as possible (raw fastq? bam files? other mutational database?) to find diseases in which this sequence is present in its mutated form.

I would greatly appreciate suggestions on how to do this.
Noa

dpryan 09-04-2014 05:37 AM

Dealing with large numbers of fastq or BAM files would take a while, so I'd just look at 1000 genomes and TCGA datasets. You should be able to just look for the variant that way without needing to do SNP calling or alignment.

Noa 09-04-2014 06:06 AM

Will try; thanks!

GenoMax 09-04-2014 06:15 AM

You can do gene specific queries against TCGA data at: http://www.cbioportal.org/public-portal/

Noa 09-04-2014 06:18 AM

brilliant! thanks, saved me a ton of searching.
anyone know of other places to do this for non-cancer diseases??


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