Question: Where can I get a GWAS data set with validated associations?
1
gravatar for haohanw
3.4 years ago by
haohanw90
United States
haohanw90 wrote:

I am working on some methods for GWAS, I want to test my method in some real GWAS data set with some validated associations, where can I find one?

It's the best if there is one for human disease, but I don't think there are open ones with validated association, probably not even open ones without validated association if I don't apply to NIH.

However, I believe that there should be some data sets for the famous plant A. thaliana, where can I find it?

Thanks.

genetics association gwas • 1.2k views
ADD COMMENTlink modified 3.4 years ago by mastal5112.0k • written 3.4 years ago by haohanw90

What do you mean with a validated association? How would you validate an association?

ADD REPLYlink written 3.4 years ago by WouterDeCoster40k

As a person on the computer science side, I cannot. And I hope that someone has collected the validated association in published work with actual wet lab experiment conducted to validate the association. @decosterwouter

ADD REPLYlink modified 3.4 years ago • written 3.4 years ago by haohanw90
1

There is no such thing as "wet lab validation of association". Furthermore, most association studies that I am aware (neurodegeneration) of are just signals from taggingSNPs, without truly finding the functional variants or explaining the disease effect. Perhaps you could consider these not validated.

ADD REPLYlink written 3.4 years ago by WouterDeCoster40k

Thank you very much. I didn't realize that. Then, if I am working on GWAS method, (like machine learning models), how should I verify that my model works?

ADD REPLYlink written 3.4 years ago by haohanw90

What is the outcome of your model? Associated loci?

ADD REPLYlink written 3.4 years ago by WouterDeCoster40k

Yes. So I hope that there are validated associated loci so that I can verify the result. (If I calculate p-value for them to verify, then basically it's going to be hard for me to convince others that my model works better than traditional p-value based methods. )

ADD REPLYlink written 3.4 years ago by haohanw90

If you are looking for strong associations from large GWAS you could try GRASP: https://grasp.nhlbi.nih.gov/FullResults.aspx. This does not give you raw individual level data per se but many strong (summary level, multi-individual) associations you could consider pursuing for functional studies.

ADD REPLYlink written 2.4 years ago by johnsonad20
0
gravatar for mastal511
3.4 years ago by
mastal5112.0k
mastal5112.0k wrote:

Have you looked at GWAS catalog?

https://www.ebi.ac.uk/gwas/home

ADD COMMENTlink written 3.4 years ago by mastal5112.0k

Thanks, but I think it's all about human diseases (mostly cancers), and I don't think I can get the relevant genotypes without a three month application to NIH or so.

ADD REPLYlink written 3.4 years ago by haohanw90
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