I am working on some GWAS (Genome-Wide Association Studies) now. A genome scan was done for all the SNPs, with first 3 principal components adjusted (PCs are used for adjusting ethnicity effect) and the QQ plot looks fine (most p-values lay on the diagonal line with a few signals off the line).
However, when I adjusted for clinical covariates (treatment, clinical stage) and rerun the genome scan, the QQ plot looks weird. Usually, when you adjust for covariates, you expect to see the p-values lay under the diagonal line (or fewer hits than unadjusted model). In my model, after adjusting for clinical covariates, the QQ plot is way off the diagonal line and almost all the SNPs are false positives. I don't know how to explain this. One important thing is that some clinical covariates are very very significant in the clinical model (the model with no SNP information), and the p-value goes to 10E-11. I have 250 samples and 750K SNPs in my dataset.