Short answer: your local Institutional Review Board has the answer you need. Consent for these studies can be a complicated issue. There's a large body of work on the ethics of genetic testing, but less that's specific to whole-genome sequencing. For a few references:

Research ethics and the challenge of whole-genome sequencing, (Nature Reviews Genetics)

Ethics watch: the G.I. genome: ethical implications of genome sequencing in the military. (Nat Rev Genet)

Ethical implications of the use of whole genome methods in medical research. (European J. Human Genetics, focuses on GWAS I think)