Dear Kyran,
I do not know about the sample sizes and the presence of comorbidity in the patient group. However, if all patients have comorbidity then you would not need a special covariate for this feature. If there are some patients with and some without comorbidity, it might be worth trying to split the patient group and run the analysis with four groups: patients with comorbidity, patients without comorbidity, controls, family. Then, you would not need to model comorbidity as a covariate at all.
Best,
Volkmar
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