Proxy Variant SNP for PRS

Question

[curious_butterfly]

Hi,

I'm relatively new to calculating PRS and I have a quick question regarding proxy variants. If SNPs that are in the GWAS are not present in my target dataset and I find proxies with high r^2 (~0.99), how do I implement this? Do I swap the proxy with the variant in the GWAS in my target data? What happens if the alleles don't match? How do I account for that?

[Sam]

Have you tried performing imputation on your target data?