BCL2 fusions not detected in RNA level

Question

[J.F.Jiang]

Hi all,

I've designed ~120bp probe panel to capture the target sequences, including BCL2, BCL6, MYC genes.

In sequencing data, we found some BCL2+ samples, which had been tested with FISH, were not detected in RNA level.

Both StarFusion and FusionCatcher were applied to detect the fusions.

It was reported that regions called MBR, MCR, icr, were previously discovered as hot breaking regions. Since regions like MCR, icr are away from gene UTR regions , we did not set the probes to cover these regions.

I am confused that why these fusions were not found in RNA levels, or these fusions can only be detectable in DNA level?

Best, Junfeng

[LChart]

The ability to detect a cDNA fusion can depend on a lot of technical factors, especially how libraries were prepared and sequenced. You will need to be more specific for anyone to really be able to answer this question without significant speculation.

[ATpoint]

Essentially, you would need to detect the breakpoint, and for this you need good coverage and the breakpoint flanks must be well-mappable. Without further details this cannot really be answered. Did you do targeted RNA-seq, please elaborate?

[J.F.Jiang]

yes, it is a target RNA probe, spanning all exons and UTR regions of BCL2, BCL6 and MYC genes.

Exon regions were well covered with more than 1000 reads.

[ATpoint]

I mean the RNA-seq, is this targeted RNA-seq or just "normal" poly-A?