Polygenic Risk Score Plot

Question

[Muhammad]

I have a dataset of about 6000 people, Chromosome 21. I calculated PRS using plink and PRSice. The plot is shown above. I have two questions regarding this.

1. R2 on the y-axis explains the phenotype variation, but I want another measure like AUC (area under the curve) for comparison with other tools.
2. What these highlighted values (1,2,3 )are representing?

Answer 1

[Sam]

You have sample overlap, i.e. sample you used for calculating the PRS were also used to estimate the effect size from the GWAS. That's why you have such inflated R2 and p-value

1. Is the p-value of association of your PRS against the phenotype of interest in the given p-value threshold (3)
2. Is the legend telling you the color w.r.t. p-value of association
3. is the p-value threshold

[Muhammad]

Hi Sam, thank you for responding and sorry for being late. Actually, there is no sample overlap.