Thanks for the links, I will check them out. An embarassing correction: the 450K is (as you well know) not a SNP array. Can you tell I've been doing more than my fair share of methylation stuff recently?

The fundamental problem I have with your reply, though, is that the authors were not really concerned with any particular SNP. They wanted to make statements about the group of ASD-related SNPs. Clearly it is infeasible to do most of the things you have suggested here with >100 SNPs. Given that, what do you suggest they should have done?