Question: What Kinds Of Hypotheses Can Be Supported By Significant Snps In A Gwas Study
1
gravatar for kumar.vinod81
6.3 years ago by
kumar.vinod81280
New Delhi
kumar.vinod81280 wrote:

Significant SNPs through GWAS are fine mapped type or we need some further work to prove the actual causative variation for the trait under study. I've done a GWAS in a plant species and identified a set of 30 SNPs showing significant signals for a susceptibility index. It means that the top most SNP is the actual cause of the trait variation or yet it need some further work to proof the actual region underlying the trait. What other we can propose with the significant SNPs? Thanks,

deleted-post • 2.9k views
ADD COMMENTlink modified 6.3 years ago by swbarnes26.0k • written 6.3 years ago by kumar.vinod81280

This question was answered and then closed . I reopened it.

ADD REPLYlink written 6.3 years ago by Pierre Lindenbaum121k

Thank you very much....in future I'll take care of it..

ADD REPLYlink written 6.3 years ago by kumar.vinod81280

"we propose to go fishing. hypothesis: we will catch something"

ADD REPLYlink written 6.3 years ago by brentp23k
4
gravatar for Jeremy Leipzig
6.3 years ago by
Philadelphia, PA
Jeremy Leipzig18k wrote:

My primitive understanding from my brief stint in agriculture is that most hits seen in plant GWAS are, in order of least common to most common:

  • the causative SNP
  • in LD with the causative SNP, you're close to it and have picked up the haplotype
  • spurious associations related to population structure effects (e.g. fungal resistance is more common in certain plant subpopulations with hairy leaves so the hairy leaf SNP is a top hit on the manhattan plot). Correcting for population effects is something of an art.

The next step I saw was positional cloning, but this was usually done in arabidopsis.

ADD COMMENTlink modified 6.3 years ago • written 6.3 years ago by Jeremy Leipzig18k

Thanks for answer. Can you please little more elaborate your answer, I am getting it but not in complete way?

ADD REPLYlink written 6.3 years ago by kumar.vinod81280
1

Here's a blog post about some of these topics...shows a couple techniques that can be used to 'bootstrap' based on the population distributions of SNPs (similar to the third recommendation by Jeremy here). http://www.cureffi.org/2013/01/29/sampling-a-matching-distribution-for-bootstrapping/

I imagine that the second problem might be solved by QTL type techniques but i am not sure exactly how

ADD REPLYlink written 6.3 years ago by cmdcolin1.2k

Thanks a lot for valuable information. The first information is really interesting and important.

ADD REPLYlink written 6.3 years ago by kumar.vinod81280
2
gravatar for Giovanni M Dall'Olio
6.3 years ago by
London, UK
Giovanni M Dall'Olio26k wrote:

The SNPs identified in a GWAS are not the real causal variant of the phenotype, but they are rather SNPs within a LD block with the real causal variant. So, sorry but you still have some work to do to discover what is causing your phenotype :-)

A few years ago, in this forum, there it has been an effort to contribute to a collaborative paper on methods for Post-GWAS functional characterization of risk loci. We started adding a section about computational methods to do such analysis. We added a general overview of the methods available, and a table of the tools that were available at the moment. Unfortunately, in the end the contributions from the online community were not taken into account :-( , and the paper was published in Nature Genetics without them. You may refer to the published paper for a reference on the functional characterization of the SNPs you have identified, and can also look at the wikigene draft for some references on the computational approaches you can use now. Anyway, if you want to look for more recent literature, you should search for the keywords Post-GWAS characterization, SNP prioritization, and candidate gene approach.

ADD COMMENTlink modified 6.3 years ago • written 6.3 years ago by Giovanni M Dall'Olio26k

Thank you very much. This is really I am searching from last few days, and now I am thinking that I will be able to do something with my GWAS results. Thanks Giovanni

ADD REPLYlink written 6.3 years ago by kumar.vinod81280
1
gravatar for swbarnes2
6.3 years ago by
swbarnes26.0k
United States
swbarnes26.0k wrote:

In order to really prove that a SNP is causative; that is, that the variant is necessary and sufficient to cause the variation observed, you need benchwork. You can't prove such a thing computationally.

ADD COMMENTlink written 6.3 years ago by swbarnes26.0k

Yes, you are absolutely right, but before my question on this blog, I was unaware in finding out the direction that where to go from here? But now I found something to go from here. Thanks a lot for your answer....

ADD REPLYlink written 6.3 years ago by kumar.vinod81280
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