These were genotyped using Illumina bead arrays (HumanHap317, HumanHap370 and HumanHap1M). BeadStudio (Illumina, San Diego, CA, USA; version 2.0) was used to call genotypes, normalise signal intensity data and establish the log R ratio and B allele frequency at every single-nucleotide polymorphism. Samples passing quality control were examined using PennCNV (10.1101/gr.6861907). Calls required 10 consecutive markers based upon the subset of markers present on all genotyping chips listed above (the HumanHap317 content). All putative de novo events were visually inspected using DosageMiner software (developed by deCODE Genetics). CNVs were excluded according to low copy repeat content and frequency as for the Bulgarian sample. This resulted in 59 CNVs, an autosomal de novo rate of 2.2%. Given the difference in the platforms, we undertook a number of analyses to confirm that the Icelandic de novos are a suitable comparator group for the case de novos (see Results and Supplementary Material).
