Identifying Split-Reads in WES data!

Question

[reza.jabal]

Hello everybody;

Here I've got a patient with an unidentified neurodevelopmental complication and primary WES analysis with candidate gene approach resulted in no significant finding. I understand that the causative mutation may reside in an intronic region, but the patient underwent good-old Karyotyping in 1999 and a balanced translocation was identified.

I was wondering if there's any practical approach to identify splitted reads at the position of translocation. I guess this could be done by investigating MRNM field in the SAM file, but is there any software that streamlines this?

Answer 1

[Garan]

We use two Exome libraries for clinical cases - Agilent SureSelect All Exon v5 and Agilent Focused Exome 16 Mb panel. We tend to use a read-depth based appraoch to call the larger structural variants (using ExomeDepth). Although I've also have found some SVs using Manta which does incorporate split read information. It does seem pretty sensitive (calling single exon HTZ deletions) however I have found it does miss SVs with deep intronic breakpoints or breakpoints well away from the nearest gene - this is not a problem with Manta but with the lack of bait coverage from the Exome library (in this case it missed a HMZ whole gene deletion easily found by the read depth approach).

I think you might have a similiar problem if your breakpont is deep intronic and not well covered by the library baits. Still give both a whirl and see what you get :)

You could always try the manual approach and review the area with IGV or Samtools if you already know the rough area of the translocation, just to confirm it's presence.

Btw which neurodevelopmental panel did you use? Tried the panelApp one(s) from 100K?

[reza.jabal]

Garan,

Thanks very much for your in-depth insight and helpful comment. I never heard of Manta and I will give it a try. Regarding the panel, we used SureSelect all Exon v5. PanelApp will definitely be useful in the future.

Once more, thank you for your time to help me with this.

Answer 2

[Sean Davis]

There are numerous softwares available for looking for translocations and other structural variants. Perhaps you want to give one of those a try?

[reza.jabal]

Hi Sean,

Thanks for your comment. Different softwares use different algorithms (Read-Pair Algorithm vs Split-read approaches & assembly based tools). Have you had any experience of working with any particular software that you'd like to recommend in this context?