Non-targeted fusions

[seq-ngs]

I am doing targeted RNA-seq using specific primers against known fusion partners (e.g., primer against BCR and primer against ABL1). I am seeing some non-targeted fusions, i.e., fusions which I am not expecting in a given sample. Some of these fusions are seen after repeat library prep and re-sequencing but most do not repeat. I am trying to think about how to interpret these - whether they are artifacts or biologically present at a low level. Does anyone have any references or approaches that they think are helpful for this?

Thanks,

seq-ngs

[nucacidhunter]

Without knowing your workflow, one possibility is contamination from other samples in the same batch or lab environment residues from previous ones. Fusions in the repeat preps could indicate contamination of input material.

You need to prevent contamination issues by physical separation of pre- and post-PCR area.