Inversion validation / confirmation

Question

[waqasnayab]

Hi,

I am wondering how to validate / confirm the existence of inversion region in other WGS samples?

For example, in one of my patient's WGS sample, I identified an inversion. Now, I want to see whether this inversion exists in other WGS samples of healthy individuals or not (I have a control dataset of around 200 WGS samples).

Deletion regions can be checked in control WGS samples by looking at their coverage, but I could not apply the same concept on inversion region.

So, how to check inversions in control samples?

Thanks in advance,

Waqas.

[ATpoint]

How did you find the inversion in the first place?

[waqasnayab]

By delly,

as far as running delly on control samples is concerned, I have only subset of those bam files (means around my inversion region), and when I run delly, empty bcf file is generated. Might delly needs at least full chromosome......

Any thing which I can do?

Answer 1

[Kevin Blighe]

Hello Waqas,

1. Standard PCR. Design separate PCR primers whose target sequences are the breakpoints for the wild-type and the inversion, respectively, and then test in the lab. If the inversion is a false-positive, then the primers for the inversion should not amplify any sequence.
2. MLPA. You could also set-up an experiment using MLPA (Multiplex ligation-dependent probe amplification), where the probes target the breakpoint
3. Real-time PCR. Design common PCR primers outside of the breakpoint but make the probe sequences specific for the breakpoint in the wild-type and inversion.
4. Sanger. Also by designing common primers outside of the beakpoint, you could just do Sanger sequencing.

Finally, read this: Validation and Genotyping of Multiple Human Polymorphic Inversions Mediated by Inverted Repeats Reveals a High Degree of Recurrence .

Kevin

[waqasnayab]

Thanks Kevin, I will try to share this information with my colleagues,!!!!