I am working on a project proposal for an exam, it involves a budget of 1M euros and I got to design a genomic study. I chose a GWAS to assess altered gene expression after covid19 that leads to long-COVID. I thought about 3 cohorts:
Case cohort1: Long-Covid patients (N: 3,000)
Case cohort2: Fully recovered patients (N: 3000)
Control cohort: healthy patients. (N: 6000)
Would it make sense to run two GWAS for the two case cohorts against the control cohort (cohort1/controls and cohort2/controls) then do a miami plot to see if there are some hits that differs from the two cohorts, and pick the ones only presented in the Long-covid for further assessment?
The study will also be supported by a validation step for both gwas. What do you think about this idea? Would it make sense or the fully-recovered patients against control cohorts is totally useless? Thank you in advance