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JonJala / mtag

Python command line tool for Multi-Trait Analysis of GWAS (MTAG)
GNU General Public License v3.0
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Replication of MTAG results #219

Open VasiliosRaptis opened 2 months ago

VasiliosRaptis commented 2 months ago

Hello,

I was wondering what is the best approach to replicate significant SNPs from a MTAG analysis.

Say I conduct MTAG on disease1 and disease2 and I am interested in disease1-specific results. My thought is to run another MTAG using independent GWAS summary statistics for disease1 ( and also for disease2? ) and use disease1-specific results to test for replication. Does this make sense?

Thanks a lot in advance Vasilis

paturley commented 2 months ago

Hello Vasilis,

When we recommended replicating significant SNPs from MTAG, I had envisioned just using a GWAS for disease 1 (if that is the disease of interest) in an independent sample. No need to pass those replication summary statistics through MTAG since part of the point of the replication is to make sure disease 2 isn't biasing your results.

Best, Patrick

On Fri, Aug 30, 2024 at 12:11 PM Vasilis Raptis @.***> wrote:

Hello,

I was wondering what is the best approach to replicate significant SNPs from a MTAG analysis.

Say I conduct MTAG on disease1 and disease2 and I am interested in disease1-specific results. My thought is to run another MTAG using independent GWAS summary statistics for disease1 ( and also for disease2? ) and use disease1-specific results to test for replication. Does this make sense?

Thanks a lot in advance Vasilis

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VasiliosRaptis commented 2 months ago

Hello Patrick,

Thanks a lot for the reply, much appreciated