chr1swallace/coloc

Summary stats of two traits are from the same dataset

Sheeya-Dong opened this issue · 6 comments

Sheeya-Dong commented

If the summary stats of two traits are from the same dataset, can coloc be used for colocalisation tests?

mocksu commented

Do you mean from the same sample?

Sheeya-Dong commented
mocksu commented

Yes. The gwas of two traits use the same samples. And if the two gwas have overlapping samples?------------------ Original ------------------From: mocksu @.>Date: Fri,Nov 3,2023 5:40 AMTo: chr1swallace/coloc @.>Cc: Sheeya-Dong @.>, Author @.>Subject: Re: [chr1swallace/coloc] Summary stats of two traits are from thesame dataset (Issue #137) Do you mean from the same sample? —Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you authored the thread.Message ID: @.> [ { @.": "http://schema.org", @.": "EmailMessage", "potentialAction": { @.": "ViewAction", "target": "#137 (comment)", "url": "#137 (comment)", "name": "View Issue" }, "description": "View this Issue on GitHub", "publisher": { @.***": "Organization", "name": "GitHub", "url": "https://github.com" } } ]

My understanding is that colocalization does not strictly require independent samples. However, due to pleiotropy and other confounding factors, you need to pay attention to your study design and use other techniques such as bi-directional two sample Mendelian Randomization to further infer causality.

Sheeya-Dong commented

Got it! Thank you!

chr1swallace commented
Sheeya-Dong commented

I got it! Thanks a lot!