We used Affymetrix 500K SNP arrays to assess CNVs in a cohort of 427 ASD cases. Details on the methods of copy number analysis and complete results are published elsewhere (3). Only the CNV result at PTCHD1 is described here. Another cohort of 996 autism probands was analyzed on 1M BeadChips (Illumina) (15). 246 male patients with ID were analyzed on a custom designed NimbleGen 385K array. Genomic DNA samples were sent to NimbleGen for the hybridizations to be performed. Each patient sample (Cy5-labelled) was co-hybridised with DNA from the reference sample NA10851 (Cy3-labelled; obtained from Coriell Cell Repository). After data normalisation, the ADM-1 algorithm (CGH Analytics 3.4, Agilent) was used for CNV discovery. The ADHD cohort was analyzed on Affymetrix 6.0 arrays. Three algorithms (Birdsuite, iPattern and Affymetrix Genotyping console (GTC)) were used to infer CNVs. The CEPH, PopGen and Ontario controls were analyzed on Affymetrix 6.0 arrays, SAGE controls were analyzed 1M BeadChips (Illumina) and Illumina 550K arrays were used for the CHOP and CAMH\GSK controls. Similar methods were used to infer CNVs in controls. The probe density
