Data from the Hap610 (cases and controls) and Hap1M (controls) platforms were processed and cleaned separately using standard procedures (see Supplementary Methods, available online). CNV calls were generated with PennCNV (version 2010-05-01)21 and iPattern22,23 using hg18 genomic coordinates. Analyses were limited to autosomal events. Trio analyses utilized the trio functions in PennCNV to improve calling accuracy and to estimate the likelihood of a de novo event.21
