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rtPCR Validated Fusion - How did it happen?

I have a RNA fusion event that we confirmed with rtPCR. The distance between the fused exons is 20 million bases, which should rule out a read-through event (correct?).

However, we don't observe unusual coverage or copy number variation in the genome.

Are there other mechanisms you can think of that would explain the presence of this fused product?

fusion rna-seq
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updated by Ram Ram • written by earonesty earonesty

What did you use to measure copy number between the fusion sites? The most likely cause of this is either a deletion between the fusion sites or a structural change (e.g., an intrachromosomal translocation). Depending on the methods used, you may or may not find these sorts of changes.

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written by Devon Ryan Devon Ryan

Hello earonesty!

We believe that this post is does not fit the main topic of this site.

Not a bioinformatics question - sorry!

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

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written by User 59 User 59

Well, I though a bioinformatic method might be applicable, looking at the RNA Seq data we already have. Maybe injecting an artificial sequence into the reference and looking at the pileup? But from the comments below and other talks other PI's, we think a wet-lab experiment, involving sequencing across custom primers, and possibly some PacBio sequencing would be the next step.

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updated by Ram Ram • written by earonesty earonesty

1 answer

So your fusion partner genes are from the same chromosome? It could possible be a result of chromosomal inversion, which in theory will not leave any traces in the copy number profile. 20Mb distance is too large for read-throughs according to data from this paper

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updated by Ram Ram • written by mikhail.shugay mikhail.shugay

Thanks! Looking into an inversion possibility now. Yeah, we ruled out a read-through. I suspect these larger chromosomal rearrangements, leaving copy-number and variation intact, are more common than we think. Gonna play with our PacBio machine to see if we can detect it.

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updated by Ram Ram • written by earonesty earonesty

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