Question about Using Effective Sample Size vs Observed Sample Size for Coloc Analysis

[laleoarrow]

Hi all,

I am currently conducting post-GWAS analysis and am planning to use Coloc for identifying shared genetic signals for two case/control gwas studies. The gwas were result of GWAS meta-analysis, which means it has different N for each SNP. I am unsure whether I should use the effective sample size (ESS) or the observed sample size (OSS) in my analysis.

Based on my understanding, the ESS adjusts for factors such as relatedness among individuals and the structure of the data, providing a more accurate measure of the statistical power and precision of effect size estimates. Additionally, in some case for a case control dataset, the proportion of samples in dataset for each SNP are not available.

Could you please advise on whether I should use ESS or OSS for Coloc analysis and provide any relevant references or guidelines?

Thank you for your assistance!

Ao