Detecting Intragenic inversions?

[simp...@gmail.com]

Hi Brian, 

I'm curious if STARFusion can detect when the inversion is within the same gene, that is for example when say exon X is flipped around? I guess on a similar note something like FLT3 ITD internal tandem repeats? Thanks as usual! 

Alex 

[Brian Haas]

Hi Alex,

STAR-Fusion doesn't currently detect these kinds of variants.  For FLT3 ITDs, there's a bunch of different specialized tools that focus on their detection.  For flipped exons, I don't think it would manifest as a skipped exon and so look more like a splicing variant from the transcriptome perspective. Sounds interesting!

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Brian J. Haas
The Broad Institute
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[simp...@gmail.com]

Thanks Brian, we only found out about it because delly on dna picked it up; its basically an inversion event of the one of the middle exons. I think I have a way to detect this but is not elegant! thanks again. 

A