Question about Covariates

[pierreyou]

Hi,

Thanks for the great work running thousands of GWAS on All of Us data.

Can you please provide a list with the covariates used in the analyses?

Cheers,
Pierre

[cvraut]

Hi Pierre,

I am also wondering the same thing.

From lines 790-799 of saige_aou.py, I think the covariates used were: age, age-squared, sex, agesex interaction, age-squaredsex interaction, and the first 20 genetic princpal components.

please correct me if I'm incorrect.

PS: It's awesome that they shared the code they used to conduct this study 🙂

[pierreyou]

Hey Chinmay @cvraut ,

Thanks for your comment.

You're totally correct. I've noticed the same thing, also sparse GRM with relatedness cutoff 0.125 has been used.
However it would be nice to have those details on All of Us website for example without digging 😅