Question: Inversion validation / confirmation
0
gravatar for waqasnayab
10 weeks ago by
waqasnayab160
Pakistan
waqasnayab160 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 9 weeks ago by Kevin Blighe30k • written 10 weeks ago by waqasnayab160

How did you find the inversion in the first place?

ADD REPLYlink written 10 weeks ago by ATpoint8.0k

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 10 weeks ago by waqasnayab160
1
gravatar for Kevin Blighe
9 weeks ago by
Kevin Blighe30k
Kevin Blighe30k 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 9 weeks ago • written 9 weeks ago by Kevin Blighe30k
1

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

ADD REPLYlink written 8 weeks ago by waqasnayab160
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