Bioinformatic analysis of exome sequenced data for gene fusions

[RNAsequestion]

Hello

I have 10 tumor DNAs sequenced for whole exome. I am interested in getting it analyzed for finding fusion genes in it. Can somebody help me analyze it for me

Thanks in advance

[golharam]

I don't think its possible to find gene fusions from DNA exome data. You would need RNA data instead. You can find SNPs with exome data but doubtful you can attribute them to gene fusions unless you had other supporting evidence.

[RNAsequestion]

Yes you are right in a way. Number of people have been sceptical. But there are number of papers in reputed journals like nature genetics etc who have identified gene fusions from exome sequence data. People have ascribing this to the reason depending upon where the breakage has occurred. Since this data is lying with me I want to take a chance and see if the analyzed data throws up some candidate genes which can be tested by RT etc. Would you be able to analyze the data or suggest somebody who can do it for me. Most definitely the person will get credit in the form of authorship etc if something meaningful comes out.

Thanks

[GenoMax]

Including the word "DNA" in your original post was what led to golharam's comment. You have 10 tumor (RNAseq) and it should be possible to look for gene fusions (https://www.biostars.org/p/45986/ and http://omictools.com/gene-fusion-detection-c141-p1.html) in that data.

[RNAsequestion]

No I dont have RNAseq data. I have DNA exome sequence data.

[RNAsequestion]

Whole Exon sequences

[GenoMax]

My apologies. What method was used to prepare the exome (capture, PCR)?

[RNAsequestion]

Sequencing libraries were generated according to the standard protocol of Illumina Inc. for high-throughput sequencing

[GenoMax]

Some discussion about this over at biostars: https://www.biostars.org/p/113591/

[golharam]

Can you tell me what papers you are referring to?

Yes you are right in a way. Number of people have been sceptical. But there are number of papers in reputed journals like nature genetics etc who have identified gene fusions from exome sequence data. People have ascribing this to the reason depending upon where the breakage has occurred. Since this data is lying with me I want to take a chance and see if the analyzed data throws up some candidate genes which can be tested by RT etc. Would you be able to analyze the data or suggest somebody who can do it for me. Most definitely the person will get credit in the form of authorship etc if something meaningful comes out.

Thanks

[RNAsequestion]

Whole-exome sequencing identifies a recurrent NAB2-STAT6 fusion in solitary fibrous tumors
Nature Genetics VOLUME 45 | NUMBER 2 | FEBRUARY 2013

[dpryan]

I remember that discussion on biostars. At the end of the day, the power to detect gene fusions with whole-exome data is incredibly low. If a study is actually interested in gene fusions from the get-go, then it should just use RNAseq.

[RNAsequestion]

Seeking Collaborator for RNASEQ Analysis for identifying fusion transcripts

Dear Bioinformatics Community:

The wisdom of sages of NG Sequencers say that it is not advisable to put efforts to analyze the whole exome (EXON) sequence data to try to find gene fusion because of the chances being very slim. I am thinking of doing RNA seq of 3 tumors. Is somebody ready to analyze that for me for gene fusions. I am open to develop collaboration and the person will get due credit.

Thanks in advance

[GenoMax]

You may want to post that as a new thread to get more visibility.