text: user12682: 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
  
  user12682: 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.
  
original_text: 12682: <p>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:</p>
  <p>Case cohort1: Long-Covid patients (N: 3,000)</p>
  <p>Case cohort2: Fully recovered patients (N: 3000)</p>
  <p>Control cohort: healthy patients. (N: 6000)</p>
  <p>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?</p>
  <p>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</p>
   12682: <p>In the end I manage to do 2 cohorts
  1: Long Covid Patients (1300N)
  2: NON Long Covid Patients that had Covid (1300).</p>
  <p>It was the most rational thing to do, and professor liked it. So that's how I manage in th end.</p>
  