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 of different microarray platforms at the PTCHD1 locus is shown in fig. S6. Fisher’s Exact Test was used to calculate the two-tailed p value.
