Can Meta-GWAS summary statistic results be used for Meta-GWAS (For example, METAL)?

Question

[li]

I know that METAL can perform meta-analysis on GWAS summary statistic files, so for Meta-GWAS
summary statistic results, can also be used for METAL's input files? The results of GWAS and Meta-GWAS
seem to be similar, so I'm a little confused. Can anyone give me some advice? I would appreciate it very much.

Answer 1

[Sam]

Yes, you can still perform meta-analysis on that. I guess the reason why some of your results are similar after meta-analysis is that the new GWAS has a smaller sample size than the original meta-analyzed GWAS thus doesn't contribute much to the final result.

Also, maybe consider fixing the formatting of the post to make it easier to read?

[li]

Thank you very much for your reply. This is the first time to ask a question in BioStar, so I am not familiar with the format of writing. Now I have made some modifications.

In fact, the reason why I want to conduct Meta-GWAS analysis on the summary statistic file of the Meta-GWAS is that sometimes the orginal GWAS summary results may not be downloadable, while Meta-analysis results can be downloaded. Therefore, I would like to know whether the results of Meta-GWAS can be combined with other GWAS summary statistic files for Meta-GWAS analysis again, and the results can be applied to my next analysis of PRS model construction.

[Sam]

If you have the Meta-analyzed results, you shouldn't need the original GWAS as its signal should be incorporated within the result.

So for example, if you have a meta-GWAS contain cohort A, B and C (e.g. A+B+C), you can then do a meta-analysis of the meta-GWAS (A+B+C) with another GWAS (e.g. D) and use the resulting GWAS for PRS calculation in an independent data set E

[li]

OK, I see. Thank you very much for your careful answer.