Requesting Insights on Potential Complex Structural Event Indicated by IGV

Question

[pragnapcu]

Hello everyone, I have come across some intriguing IGV patterns that suggest a complex structural event. Here's a summary of the key observations:

1. The coverage track shows a region that appears duplicated (noted by a red highlight), indicating exon duplications.
2. The flanking regions of these exons exhibit soft clipping, with multiple mismatched alignments over the reads. This mismatched region aligns perfectly with the intronic region of another gene on the same chromosome.
3. Also, the mates of some reads are mapped to the same intronic region of a different gene on the same chromosome, which may suggest a long-range effect or translocation event (indicated by 2 marked in red).
4. Please note the distantly mapped read pairs, as indicated by 1 marked in red. I'm considering the possibility of a complex structural event. Does anyone have experience with such patterns or can offer insights into potential mechanisms at play here?

Answer 1

[wakaruszka]

Hi, pragnapcu Let me try to explain what you have in your data. It looks like the exons of the gene are duplicated, but the introns are deleted. The breakpoints are exactly at the exon-intron boundaries of the gene.

These reads likely originate from a processed pseudogene that has no introns (like cDNA). More information can be found here http://dx.doi.org/10.1016/j.jmoldx.2015.05.005 and here doi:10.1002/humu.23845.

I recommend you to use the option in IGV: Sort by insert size. It helps to visualize your data better. Good luck