Question: about GWAS studies and causal variants
2
gravatar for Bogdan
10 weeks ago by
Bogdan850
Palo Alto, CA, USA
Bogdan850 wrote:

Dear all,

thought that i could ask you please : from a series of Genome Wide Association Studies, we can see some variants that are associated with an ocular disease, that are LoF (Loss of function) or PVT (trigger protein truncations).

what is the chance of these LoF or PVT variants to be causal, instead of only associated with the phenotype ? thanks a lot !

-- bogdan

snp gwas • 142 views
ADD COMMENTlink modified 10 weeks ago by WouterDeCoster40k • written 10 weeks ago by Bogdan850

Good question. Mark and wait for the answers from experts.

ADD REPLYlink written 10 weeks ago by Shicheng Guo7.7k
1
gravatar for WouterDeCoster
10 weeks ago by
Belgium
WouterDeCoster40k wrote:

what is the chance of these LoF or PVT variants to be causal, instead of only associated with the phenotype ?

A first thing you can look at is their frequency. If your disease is very rare, but your LOF variants are common (which is usually the case in GWAS) then it is unlikely to be causal. Second, it's worth checking if you can find unaffected individuals without the disease, which would argue for an association rather than causal, depending on the penetrance. The third question could be to see if the proteins can be linked to ocular diseases. A protein only active in sperm, or kidney, or muscle, is unlikely to be your variant of interest.

But eventually, you'll have to do some functional validation in the lab to show the role of this variant in the disease.

ADD COMMENTlink written 10 weeks ago by WouterDeCoster40k
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