What is the significance threshold of PheWAS plots?

General
1

Hi,

Thank you for this wonderful resource. Could you please specify what is the significance threshold in the PheWAS plots, and how it was obtained? It appears to be around 1.3e-5 but I could not find it in the documentation.

Thanks in advance!

Adil

2

Hi @Adil_Harroud, and welcome to the Open Targets Community! :tada: :partying_face:

Only traits with P-value < 0.005 are returned on the PheWAS plot. I’m not sure if this answers your question?

Best wishes,

Helena

3

Thank you for your reply. On the PheWAS plots (example attached), there is a horizontal red line near 10-5 on the y axis (p-values). Does this red horizontal line represent a certain significance threshold for the PheWAS? If so, what is this significance threshold and how was it obtained? Alternatively, could you provide the number of traits tested for FinnGen + UKB + GWAS Catalog?

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4

Hi Adil,
the red horizontal line you refer to denotes the significance level after Bonferroni correction for the number of phenotypes testing, conservatively considering each as independent.
This value is different from the PheWAS inclusion pvalue < 0.005 that was mentioned in the previous response.

I hope this helps!

You can find more info on the data and analyses included in the Genetics Portal in our documentation pages.

Best wishes,
Annalisa