We have a small study (100+ cases) in which we did not collect controls (main interest is in somatic variation). What approaches would folks suggest trying in such a situation to do a GWAS-lite analysis (this would be a hypothesis-generating exercise....)? In particular, can 1kg data be used for the controls?
These are naive questions, I know, but our study design leaves a bit to be desired and I haven't found a good reference that matches our situation.
You say you're interested in somatic variants. Are you looking at paired tumor/normal data?
We have paired tumor/normal data, yes. The GWAS is to look for disease predisposition in the germline genotypes.