I begin to calculate polygenic risk scores. And i have had some problems. Gwas summary results were obtained from European samples, and they were used to calculate polygenic risk score in east asian samples. Results show that the performance is poor. There are many reasons for this, such as allele frequency, LD etc. Can someone know how to adjust SNP effect size or other ways for better performance in target samples?
- Population consideration
The most appropriate method is to use summary statistics from a discovery population corresponding to the ethnicity of your target group
However, If they are not available, You may consider using either unweighted GRS (SNP's weights will be assigned equally) or weighted GRS with multi-ethnic summary statistics (SNP's weights will be averaged globally).
- Model Performance
If you have whole-genome summary statistics, what about clumping it with different thresholds and evaluating the predictive ability of those candidate summary statistics. As a result, you will get the most optimal model with highest performance.