I particularly like the following discussion on validation.
Conard: How do you go about validating the output information?
Cardon: I think there are two levels to validation. The one that probably gets overlooked most often is quality control. The first thing you want to look at is quality of the genotypes. Before you expend all that effort and spend the money, some mechanism for validating the genotype is important. That may mean re-genotyping, but it would be re-genotyping a relatively small number of markers and potentially using a different assay to really validate those findings before going further.
The second level concerns replication—the gold standard in association studies. When someone reports a finding, the best thing that can happen is someone in a different lab says, “I genotyped that same marker on my samples and I saw the same results.” That happened with macular degeneration recently, and that’s very hard to argue against.