Samples were genotyped using the Illumina Human 1M-single Infinium BeadChip. We performed stringent, uniform QC procedures on the resulting data. The Illumina Human 1M-single Infinium BeadChip contains a total of 1 072 820 markers (50-mer probes) for SNP and CNV analyses. Samples were processed using the manufacturer's recommended protocol with no modifications for Infinium II arrays, and BeadChips were scanned on the Illumina BeadArray Reader using default settings. Analysis and intra-chip normalization were performed using Illumina's BeadStudio software v.3.3.7, with a GenCall cutoff of 0.1. Built-in controls, both sample independent (including staining controls, extension controls, target removal controls and hybridization controls) and sample dependent (including stringency controls, nonspecific binding controls and nonpolymorphic controls), were inspected to assess the quality of the experiment. For genotype calling, we followed the manufacturer's protocols and used technical controls. Trios consisting of an affected offspring and both parents were genotyped, and in total genotyping was completed for 4683 individuals from 1558 families. For the control sample, 1880 individuals were genotyped on the Illumina Human 1M-single Infinium BeadChip, as described elsewhere (23).
