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?
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dandanli0365 •
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).
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.
Thank you and both methods are great. But i still feel a little confused. How can i get multi-ethic summary statistics? which website can download it?
you can explore the summary statistics from GWAS catalog or a public consortium such as cardiogram (coronary artery disease).
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I don't believe there is anything to do this, currently. Obviously the ethnic groups should match.
You may consider either of the following:
Kevin
thank you very much, could you please give me a paper about scores based on population differences?