Their basis is correlation. An excerpt from an article on the recent
study:
As the team notes in their paper, it is still very difficult to make the connection between the areas that the de novo CNVs hit and the genes these areas harbor. Nor is it clear what role those genes have in perturbing the biology of the developing brain, giving rise to autism. In the associated paper, Vitkup, Iossifov and others use a novel form of analysis called NETBAG (network-based analysis of genetic associations) to identify “the large biological network of genes affected by rare de novo CNVs in autism.” They note that this network is strongly related to genes previously implicated in studies of autism and intellectual disability. And they specify that the genes in question relate primarily to the development of synapses, the junctions between brain cells which are their transmission nodes; as well as the targeting of axonal fibers and the ability of young neurons to migrate. All are essential aspects of brain development.
Subsequent sequence-based studies should be able to further resolve individual genes within the CNV regions, and significantly expand the list of candidate genes for autism. Even now, however, the data on spontaneous CNVs and a separate but also an important class of “ultra-rare” CNVs that were inherited by some of the affected children in the sample, reveal interesting and in some cases vexing “asymmetries,” the team reported.
Among these asymmetries: spontaneous causal CNVs were found in 8% of the affected children in the sample; this is four times their rate of occurrence in unaffected siblings. Since CNVs occur with equal frequency across the human population – we all have them, but in most of us the missing or extra genetic material doesn’t hit essential genes or contribute to illness – the fact that they are seen four times as often in affected children as in their unaffected siblings points to their likely contributory role in the illness.
They don't know
what role those genes have in perturbing the biology of the developing brain, giving rise to autism.
The author of the study also notes that the causes of autism are likely diverse:
“The causes of autism when fully fleshed out are likely to be very diverse,” Wigler says, “some of which may be treatable much more readily than others. However, the diversity of causes implies that an effective future treatment for one form of ASD may be specific only for a narrow subset of those affected.”
Note that in his description of diverse causes, he does not limit the causes to being genetic.