What software to use for GWAS with repeated longitudinal quantitative phenotype data?

Question

[hkj7]

I have quantitative data that has been collected at 4 different time points. Before treatment, 1 month after, 1 year after and 2 year after.

I have generated Linear Mixed Models in R to obtain the residuals. I am not sure what software to use to carry out the genetic association analysis test. I have PLINK genotype files. PLINK software only looks at genotype-phenotype associations for cross-sectionally measured phenotypes.

From what I understand GCTA software accounts for related individuals rather than repeated phenotype data. GMMAT is an R package for binary outcomes RATHER than quantitative. I am really unsure which software to use.

Any help would be greatly appreciated!