Hello everyone,
I have some Bionano data which says that a deletion is causing a PAX5::ZCCHC7 gene fusion. We have some RNASeq data processed with STAR fusion data saying there is 1921 supporting reads for this gene fusion. However, how can a deletion cause this fusion when the two genes are on opposite strands? An inversion could cause this, but a deletion causing this makes no sense. Am I missing something here?
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the strongest evidence for it being a "true gene fusion" would be probably be RNA-seq data with spliced reads joining the exons of both genes. you can try something like FusionInspector which shows the data on "fusion contigs" https://github.com/FusionInspector/FusionInspector. and indeed, like you say, if the RNA-seq data is truly joining the two genes, the might be an inversion type SV since it would be very unusual for a gene product to be formed from opposite strands.
schematic of fusion inspector from wiki
result of fusion inspector, showing 'sashimi arcs' between the two gene models, indicative of a fusion
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