Is it possible to perform meta-analysis of gene-based LMM tests for a binary trait?
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6.3 years ago
Nick ▴ 70

Hi everyone,

We have exome-chip data (disease cases and healthy controls) from three different studies.

Currently, for each study I have performed group-based tests (CMC test, variable threshold test and SKAT-O) using a LMM to adjust for population structure (via a kinship matrix - tests performed using EPACTS software).

However, I cannot find an appropriate software to perform meta-analysis on these results. Does anybody know if such a software exists?

As far as I can tell, existing software for meta-analysis of gene-based tests (e.g. RAREMETAL, metaSKAT, seqMeta) requires genotype data as input, and calculates initial scores from each study before combining them in a meta-analysis. This suggests I won't be able to use the results of my kinship-adjusted LMM tests(?). I am also concerned that some of these methods may not be appropriate for use with binary traits and would only be suitable for continuous traits.

Is there a good reason why I can not just run a simple meta-analysis using METAL (for example), in the same way that I would for a single marker test? Otherwise, what options are open to me?

Any advice or recommendations would be much appreciated!

Thanks,

Nick

meta-analysis SKAT Burden tests LMM SNP • 2.0k views
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