GCTA tool for case-control association analysis

Question

[seta]

Dear all,

I found here, GCTA is a suitable tool for doing association analysis of both related and unrelated samples as it account for sample relatedness yes? But the MLM (mixed linear model) option within GCTA is just for quantitative traits, could you please let me know if there is any option to analysis case-control (binary trait)?

Thanks

Answer 1

[Lemire]

I was the one suggesting GCTA in addition to GEMMA to deal with relatedness. I am not as familiar with GCTA, but GEMMA deals with case/controls as if it was a quantitative trait, using the following justification (from the manual):

"For binary traits, one can label controls as 0 and cases as 1, and follow our previous approaches to fit the data with a linear mixed model by treating the binary case control labels as quantitative traits [? ? ]. This approach can be justified partly by recognizing the linear model as a first order Taylor approximation to a generalized linear model, and partly by the robustness of the linear model to model misspecification [? ]."

This workaround was, I believe, an implementation convenience from the point of view of efficiency. You could use the same argument if using GCTA.