Colocalization of eQTL and GWAS

[cy6n]

Hi Chris,

Thanks for making this fantastic package!

I am working on the colocalization analysis with fine mapping using eQTL and GWAS. And I got some questions when I use this package.

Currently, I have the fine-mapping results of eQTL coming from our collaborators. For example, for one specific gene, we have a credible set including two putative causal variants. And then I did my own fine mapping using SuSIE (susie_rss) for this region (position of this gene +/- 1MB) at GWAS and I got one credible set including 25 putative causal variants.

However, there is only one common/overlap SNP at the fine-mapping result of GWAS and eQTL. Could I use this one specific SNP to do the coloc.abf? And if I got two common/overlap SNPs from the fine-mapping of GWAS and eQTL. Could I use these two SNPs to conduct the coloc.susie by using their LD martix?

Greatly appreciate your help!

Best, Chaojie

[mocksu]

Did you check the genomic coordinates of your datasets? They might be in different versions (e.g. hg37 vs hg38).

[chr1swallace]

coloc evaluates different hypotheses including no causal variants for either trait, so you need statistics for variants that cover the whole region of interest in both traits, not just the intersection of independent fine mapping.

[cy6n]

Did you check the genomic coordinates of your datasets? They might be in different versions (e.g. hg37 vs hg38). Thanks for your reply.

Yes -- they are in same version (hg38)

[cy6n]

coloc evaluates different hypotheses including no causal variants for either trait, so you need statistics for variants that cover the whole region of interest in both traits, not just the intersection of independent fine mapping.

Thanks for your responses and that is very helpful. However, I was wondering why we need to apply the color_susie if coloc evaluates different hypotheses including no causal variants for either trait?

[chr1swallace]

Because coloc.abf doesn't allow for more than one casual variant per trait. Coloc.susie allows for that

https://chr1swallace.github.io

---

From: cy6n @.> Sent: Thursday, March 9, 2023 9:58:49 PM To: chr1swallace/coloc @.> Cc: Chris Wallace @.>; Comment @.> Subject: Re: [chr1swallace/coloc] Colocalization of eQTL and GWAS (Issue #114)

coloc evaluates different hypotheses including no causal variants for either trait, so you need statistics for variants that cover the whole region of interest in both traits, not just the intersection of independent fine mapping.

Thanks for your responses and that is very helpful. However, I was wondering why we need to apply the color_susie if coloc evaluates different hypotheses including no causal variants for either trait?

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