The AGP Consortium, which represents more than 50 centers in North America and Europe, collected data from 1558 ASD families (4712 subjects) for this study (Supplementary Material, Table S1). Both Autism Diagnostic Interview-Revised, ADI-R (2), and Autism Diagnostic Observation Schedule, ADOS (3), were used for research diagnostic classification. Nested research classification of subjects into ‘strict’ or ‘spectrum’ (i.e. encompasses strict) was developed based on ADI-R and ADOS classification. Subjects with known karyotypic abnormalities, fragile X mutations or other genetic disorders were excluded. Genotyping was performed by using the Illumina Human 1M-single Infinium BeadChip array. A total of 1369 ASD families comprising 1385 ASD probands (Table 1) passed quality control (QC) filters (Supplementary Material, Table S1). Counting up to third-degree relatives in the 1369 families, 43.6% had two or more ASD children (multiplex), 42.4% had one affected child (simplex) and 14% were unknown (extended family not evaluated); note, however, that we typically genotyped only one proband per family, as well as parents, even if the family were multiplex. Proband distribution by gender was 84% male and 16% female; 58.6% attained a
