Question: Full intronic deletions on a Whole-Exome Sequencing experiment
gravatar for bdelolmo
2.9 years ago by
bdelolmo10 wrote:


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,

Full-intronic deletion

ADD COMMENTlink modified 2.9 years ago by trausch1.4k • written 2.9 years ago by bdelolmo10

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

ADD REPLYlink written 2.9 years ago by WouterDeCoster42k
gravatar for trausch
2.9 years ago by
trausch1.4k wrote:

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.

ADD COMMENTlink written 2.9 years ago by trausch1.4k
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