Finally, we investigated whether different classes of genes or regions -- loci previously implicated by functional or positional candidate gene association studies, rare variants implicated in autism, Mendelian disorder genes with association to autism, or regions of copy number variation associated with autism -- showed association with common alleles included in our marker set. Although there were several nominally significant associations, only the Williams syndrome region (one SNP in GTF2IRD1) was borderline statistically significant (P = 0.051), after correcting for the microdeletion/duplication syndrome regions tested. In the category of Mendelian disorders associated with autism, MECP2, the gene for Rett syndrome, showed region-wise statistical significance. These results raise the possibility that Rett and Williams syndrome genes may contribute more generally to autism spectrum disorders. Although the genes in which common variation has been reported to be associated with autism do not show evidence for association, this cannot be interpreted as failure to replicate previous results in all cases, because much of the variation reported as associated is not captured on the Affymetrix platform (e.g. length polymorphisms, microsatellites, untagged SNPs such as
