Question: Selection of a "suggestive" level of association in a GWAS study
4
gravatar for Vincent Laufer
4.4 years ago by
Vincent Laufer1.1k
United States
Vincent Laufer1.1k wrote:

In GWAS studies, 5*10-8 seems the defacto standard for association. A lesser known threshhold is 1*10-5.

This threshhold is often called "suggestive association."

I am writing to ask, where did this figure come from? Were empirical tests or statistical simulations done to select this level? 

I can find many papers that USE this level, but far fewer that JUSTIFY it. Any relevant citations would be welcome, and thank you.

statistics association gwas • 3.1k views
ADD COMMENTlink modified 4 months ago • written 4.4 years ago by Vincent Laufer1.1k
2
gravatar for lindsay.leek
4 months ago by
lindsay.leek30
lindsay.leek30 wrote:

"The P values of Bonferroni corrected thresholds for suggestive, 5 and 1% genome-wide significant levels were 1, 0.05 and 0.01, respectively, divided by the number of SNPs used in the GWAS. The suggestive level was first proposed by Lander and Kruglyak [17] and represents the threshold where, under the null hypothesis, one false positive is expected per genome scan."

So the suggestive line is calculated as the -log10( 1 / number of variants)

Reference: Guo, Y., Huang, Y., Hou, L., Ma, J., Chen, C., Ai, H., ... & Ren, J. (2017). Genome-wide detection of genetic markers associated with growth and fatness in four pig populations using four approaches. Genetics Selection Evolution, 49(1), 21.

ADD COMMENTlink modified 4 months ago by zx87548.2k • written 4 months ago by lindsay.leek30

this is interesting - of course the bulk of the literature of which I am aware derives an understanding of these levels from the number of effectively independent markers.

so would be odd to use a pig based threshold unless they have similar levels of LD and numbers of haploblocks

ADD REPLYlink written 4 months ago by Vincent Laufer1.1k
1

Hi Vincent,

I added the paper because of " was first proposed by Lander and Kruglyak [17] " to indicate that they were the first to propose this. If you go to the paper of Lander Kruglyak, you will find a more precise explanation of the suggestive linkage. Good luck!

ADD REPLYlink written 3 months ago by lindsay.leek30

Thank you for clarifying, lindsay!

ADD REPLYlink written 3 months ago by Vincent Laufer1.1k
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