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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

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In the end I manage to do 2 cohorts 1: Long Covid Patients (1300N) 2: NON Long Covid Patients that had Covid (1300).

It was the most rational thing to do, and professor liked it. So that's how I manage in th end.

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