Full intronic deletions on a Whole-Exome Sequencing experiment

Question

[bdelolmo]

Hello,

I am interested in analyzing Structural Variation in a set of samples from a WES experiment. I have used Pindel and Delly, and surprisingly I have found weird breakpoints in some genes that indicate a full deletion of the intronic regions. Does anyone know if this is an artifact? I was thinking in a false prediction due to a pseudogene without intronic sequences, but I checked the exon-exon junction sequences (BLAT) and they mapped uniquely. This event is quite frequent (pict attached)

Many thanks,

[WouterDeCoster]

First thing that comes to my mind is RNA contamination, but how would something like that happen...

Answer 1

[trausch]

This is indeed most likely due to a processed pseudogene. The breakpoint sequence can still map uniquely if the processed pseudogene is not part of the reference. That's why it was actually called as a deletion by Delly, I think.