Where can I get a GWAS data set with validated associations?
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6.2 years ago
haohanw ▴ 90

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.

gwas association genetics • 1.9k views
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What do you mean with a validated association? How would you validate an association?

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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

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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.

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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?

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What is the outcome of your model? Associated loci?

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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. )

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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.

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6.2 years ago
mastal511 ★ 2.1k

Have you looked at GWAS catalog?

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

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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.

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