After applying QC filters, 775,311 common autosomal SNPs remained in the discovery dataset with an average genotyping rate of 99.80% and 500,100 common autosomal SNPs remained in the validation dataset with an average genotyping rate of 99.82%. To account for possible population stratification, we excluded families if the values for the top two principal components for either of the probands' parents were > 4 standard deviations from the core Caucasian cluster generated in EIGENSTRAT (Patterson, Price & Reich 2006). The final datasets included 1,390 samples from 438 autistic families in the discovery dataset and 2,390 samples from 457 autistic families in the validation dataset. For any SNP of interest in the discovery dataset not directly genotyped in the validation dataset, imputation of genotypes was performed in the validation dataset using the program IMPUTE (Marchini et al. 2007). The Pedigree Disequilibrium Test (PDT) (Martin et al. 2000, Martin, Bass & Kaplan 2001) was used for all association analyses. The distribution of p-values examined in the discovery dataset demonstrated a close match to that expected for a null distribution except at extreme
