Question: Inversion validation / confirmation
0
gravatar for waqasnayab
4 months ago by
waqasnayab170
Pakistan
waqasnayab170 wrote:

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.

ADD COMMENTlink modified 4 months ago by Kevin Blighe33k • written 4 months ago by waqasnayab170

How did you find the inversion in the first place?

ADD REPLYlink written 4 months ago by ATpoint11k

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?

ADD REPLYlink written 4 months ago by waqasnayab170
1
gravatar for Kevin Blighe
4 months ago by
Kevin Blighe33k
Republic of Ireland
Kevin Blighe33k wrote:

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

ADD COMMENTlink modified 4 months ago • written 4 months ago by Kevin Blighe33k
1

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

ADD REPLYlink written 3 months ago by waqasnayab170
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