I am working with the output of STAR-Fusion, looking to define fusion events in a panel of cell lines.
Genes are annotated as fused with LeftGene or RightGene i.e. GeneA-GeneB fusion vs GeneB-GeneA fusion.
I am looking to determine if an A-B fusion has the same effect as a B-A fusion.
I have read a paper on fusions that suggests a) directionality of fusions is important in determining their effect, and b) whilst A-B fusions may produce an in-frame fusion transcript, B-A fusions may not. I'm assuming that the out-of-frame transcripts will therefore be degraded by NMD or other processes, leading to lower representation in RNA-Seq data?
My question is, is there a way to annotate the STAR-Fusion output to determine which of the A-B and B-A fusion products are creating functional proteins after translation? Does A-B or B-A create an in-frame transcript? Similar to a variant effect predictor with mutations?
e.g. would the BCR-ABL1 fusion have the same oncogenic effect in CML as the ABL1-BCR fusion?
