How was LD clumping performed to select eQTLs for candidate gene?

I am wondering How LD clumping was performed to select eQTLs for candidate gene in eQTL-based two-sample Mendelian Randomization? How to handle pleiotropy eQTL issue? for example, a SNP is eQTLs for candidate gene, but also for multiple other genes? Do we have any strategy to select gene-specific eQTL?

This question was originally asked on GitHub and has been posted here so that answers can benefit the whole community of users.

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We have not used eQTLs for performing Mendelian Randomization analyses so far.

However, we do perform genetic colocalisation analyses using eQTLs. For this, we use GCTA, along with LD from the UK Biobank, to identify conditionally-independent signals for both eQTLs and for GWAS (limited to European ancestry studies). We then do colocalisation tests between all pairs of signals that have an overlap in their 95% credible sets.

So the short answer to your question is that we haven’t done those analyses. When looking at eQTL colocalisations, you will find results for coloc tests against all genes whose credible set overlaps, which in some cases will be multiple genes at a locus.

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It is a great question. I am wondering is there any plan that OpenTarget perform this eQTL-based MR analysis?

Meanwhile, I’d like to share Dr. Mike Love’s comments on:

How LD clumping was performed to select eQTLs for candidate gene?


Share an interesting analysis which I think will be useful for OT platform:

ExPheWas: a platform for cis-Mendelian randomization and gene-based association scans