LD reference panel for using PoPS on cross-ancestry meta results

[zhangchuyi]

Hello PoPS team,

I want to use PoPS on a cross-ancestry meta-analysis results (40k cases + 370k controls European samples & 4k cases + 10k East Asian samples) where the European samples make up the overwhelming majority.

Since the LD information was included in the models, I was confused what LD reference panel should I use? a European only LD, or a LD calculated in a mixed population (like 1000G), or a weighted integration LD from EUR and EAS, or should I do the MAGMA part separately for each ancestry and then meta the MAGMA results?

Could you please give me some advances on this issue?

Thank you!