Replication of MTAG results

[VasiliosRaptis]

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]

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

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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 — Reply to this email directly, view it on GitHub <#219>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AFBUB5LP6QHB6XYTAPD2NF3ZUCKSJAVCNFSM6AAAAABNMYLC26VHI2DSMVQWIX3LMV43ASLTON2WKOZSGQ4TONRXGIZTAMA> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[VasiliosRaptis]

Hello Patrick,

Thanks a lot for the reply, much appreciated